bluuebunny/crossref_metadata_2025 huggingface dataset:
Terahertz quantum-cascade lasers for high-resolution spectroscopy of sharp absorption lines
Authors: Röben B. , Lü X. , Biermann K. , Schrottke L. , Grahn H. T.
Published: April 2019

Terahertz (THz) quantum-cascade lasers (QCLs) are currently unparalleled for high-resolution spectroscopy of very sharp absorption lines (linewidths below 100 MHz) in the range between 2 and 5.4 THz. Since the frequency range accessible by a single QCL is determined by its typically very limited tuning range, a particular QCL has to be fabricated for each specific application. We quantitatively analyze the frequencies of the modes in THz QCLs with a Fabry–Pérot resonator as a function of its length taking into account waveguide dispersion. Based on these results, we develop a process based on mechanical polishing of the front facet to adjust the emission frequency with a precision of 1 GHz. The demonstrated process makes it possible to reliably fabricate THz QCLs for the spectroscopy of very sharp absorption lines.
Chaos in a ring circuit
Authors: Farcot E. , Best S. , Edwards R. , Belgacem I. , Xu X. , Gill P.
Published: April 2019

A ring-shaped logic circuit is proposed here as a robust design for a True Random Number Generator (TRNG). Most existing TRNGs rely on physical noise as a source of randomness, where the underlying idealized deterministic system is simply oscillatory. The design proposed here is based on chaotic dynamics and therefore intrinsically displays random behavior, even in the ideal noise-free situation. The paper presents several mathematical models for the circuit having different levels of detail. They take the form of differential equations using steep sigmoid terms for the transfer functions of logic gates. A large part of the analysis is concerned with the hard step-function limit, leading to a model known in mathematical biology as a Glass network. In this framework, an underlying discrete structure (a state space diagram) is used to describe the likely structure of the global attractor for this system. The latter takes the form of intertwined periodic paths, along which trajectories alternate unpredictably. It is also invariant under the action of the cyclic group. A combination of analytical results and numerical investigations confirms the occurrence of symmetric chaos in this system, which when implemented in (noisy) hardware, should therefore serve as a robust TRNG.
Spatial modulation of heat source for highly sensitive photothermal detection
Authors: Dong Jingtao , Zhang Tengda , Zhang Yuzhong , Yang Lei , Lu Rongsheng
Published: April 2019

Characterization of the weak absorption loss of optical materials requires highly sensitive photothermal detection. To address this requirement, the temperature field induced by a spatially modulated Gaussian heat source imposed on an optical glass is analyzed and compared with that induced by the same heat source modulated temporally. The theoretical analysis reveals that the temperature variation due to the spatial modulation (SM) of the heat source is much larger than that due to the temporal modulation (TM) because the irradiated site not only has a high temperature peak in the quasi-steady state of heating but also has a temperature valley as low as the ambient temperature. This distinct advantage allows for a stronger thermoelastic response of the material and accordingly highly sensitive photothermal detection. The results of the experiment on a fused silica glass verified that the photothermal image due to the SM shows up the weak absorptive defects that have not appeared in that due to the TM under the same experimental conditions. The improvement in the sensitivity is calculated to be 1.8, and the degradation of the sensitivity due to the inevitable experimental imperfections is finally discussed.
Experimental study of single-particle trapping mechanisms into microcavities using microfluidics
Authors: Shen F. , Xue S. , Xu M. , Pang Y. , Liu Z. M.
Published: April 2019

Single-particle trapping mechanisms into microcavities are still puzzling for size-based particle/cell sorting in microfluidics. Aiming to verify the prediction of particle-wall collision trapping mechanism, we explore the effects of the microcavity trailing wall on the single-particle trapping behaviors for various microcavity aspect ratios (λ = 0.5–5) and inlet Reynolds numbers (Re = 5–400), uncovering three new trapping phenomena, namely, contact trapping, collision trapping, and rapid trapping. We characterize the particle velocity variation during the trapping process. We also investigate the separatrix topology (streamlines between the microvortex and microchannel flow) and map the different particle trapping phenomena. The particle trapping results from the combined effects of the microcavity trailing wall, the separatrix topology, and the particle dynamics. The results provide new insight into the fundamental understanding of particle trapping mechanisms and could guide the applications of microcavity-based microfluidics.
THz frequency- and wavevector-dependent conductivity of low-density drifting electron gas in GaN: Monte Carlo calculations
Authors: Syngayivska G. I. , Korotyeyev V. V. , Kochelap V. A. , Varani L.
Published: April 2019

We report the results of the Monte Carlo simulation of electron dynamics in stationary and space- and time-dependent electric fields in compensated GaN samples. We have determined the frequency and wavevector dependencies of the dynamic conductivity, σω,q (i.e., the electron response to high-frequency electrical signals). We have found that the spatially dependent dynamic conductivity of the drifting electrons can be negative under stationary electric fields of moderate amplitudes, 2..5kV/cm. This effect is realized in a set of frequency windows. The low-frequency window with negative dynamic conductivity is due to the Cherenkov mechanism. For this case, the time-dependent field induces a “traveling wave” of the electron concentration in real space and a “standing wave” in the energy/momentum space. The higher frequency windows of negative dynamic conductivity are associated with the optical phonon transient time resonances. For this case, the time-dependent field is accompanied by oscillations of the electron distribution in the form of the “traveling” waves in both the real space and the energy/momentum space. We discuss the optimal conditions for the observation of these effects. We suggest that the studied negative dynamic conductivity can be used to amplify electromagnetic waves at the expense of energy of the stationary field and current.
Acceleration of plasma in current sheet during substorm dipolarizations in the Earth's magnetotail: Comparison of different mechanisms
Authors: Parkhomenko Elena I. , Malova Helmi V. , Grigorenko Elena E. , Popov Victor Yu. , Petrukovich Anatoly A. , Delcourt Dominique C. , Kronberg Elena A. , Daly Patrick W. , Zelenyi Lev M.
Published: April 2019

This work is devoted to the investigation of particle acceleration during magnetospheric dipolarizations. A numerical model is presented taking into account the four scenarios of plasma acceleration that can be realized: (A) total dipolarization with characteristic time scales of ≈3 min; (B) single peak value of the normal magnetic component Bz occurring on the time scale of less than 1 min; (C) a sequence of rapid jumps of Bz interpreted as the passage of a chain of multiple dipolarization fronts (DFs); and (D) the simultaneous action of mechanism (C) followed by the consequent enhancement of electric and magnetic fluctuations with the small characteristic time scale ≤1 s. In a frame of the model, we have obtained and analyzed the energy spectra of four plasma populations: electrons e−, protons H+, helium He+, and oxygen O+ ions, accelerated by the above-mentioned processes (A)–(D). It is shown that O+ ions can be accelerated mainly due to the mechanism (A); H+ and He+ ions (and to some extent electrons) can be more effectively accelerated due to the mechanism (C) than the single dipolarization (B). It is found that high-frequency electric and magnetic fluctuations accompanying multiple DFs (D) can strongly accelerate electrons e− and really weakly influence other populations of plasma. The results of modeling demonstrated clearly the distinguishable spatial and temporal resonance character of particle acceleration processes. The maximum particle energies depending on the scale of the magnetic acceleration region and the value of the magnetic field are estimated. The shapes of energy spectra are discussed.
Domain wall induced modulation of low field H-T phase diagram in patterned superconductor-ferromagnet stripes
Authors: Bhatia Ekta , Barber Zoe H. , Maasilta Ilari J. , Senapati Kartik
Published: April 2019

We present a systematic study of the magnetic domain wall induced modulation of superconducting transition temperature (Tc) in Nb/Ni bilayer stripes. By varying the thickness of the Ni layer from 20 nm to 100 nm we have been able to measure the low field Tc-H phase diagram spanning the Néel domain wall and Bloch domain wall range of thicknesses. Micromagnetic simulations confirmed a stronger out-of-plane stray field in the Bloch domain walls compared to the Néel walls. A suppression in Tc was observed in the magnetization reversal region of the Ni film, the magnitude of which followed linearly to the strength of the out-of-plane stray field due to the domain walls. The upper limit of the magnitude of domain wall stray field was roughly estimated by comparing the Tc of the suppressed region of H-Tc phase diagrams with the unaffected part of the H-Tc curve. With Bloch domain walls a change in Tc of more than 60 mK was observed which is much more compared to the earlier reports. We believe that the narrow stripe geometry of the bilayers and the transverse external field maximized the effect of the domain walls in the Ni layer on the overlying superconducting film, leading to a larger change in Tc. This observation may be useful for domain wall controlled switching devices in superconducting spintronics.
Experimental investigation on radiation characteristics of RF electromagnetic pulse from atmospheric spark discharge plasma
Authors: Yan Jiangzehui , Xu Luping , Tie Weihao , Jiang Dan , Yan Bo
Published: April 2019

RF electromagnetic pulses (EMPs) generated from gas discharge can not only cause serious interference or damage to electronic equipment but also be utilized in many new applications. In this paper, we establish an experimental platform for studying radiation characteristics of RF EMP from spark discharge plasma at atmospheric pressure. The influences of discharge voltage, electrode configuration, and storage capacitance on the amplitude-frequency characteristics of RF EMP are analyzed. A combined dipole-loop antenna model is proposed to describe the radiation process of EMP from spark discharge plasma. The results show that the frequency spectrum of RF EMP from spark discharge plasma mainly focuses on three intervals, namely, (0–50) MHz, (50–100) MHz, and (100–200) MHz. The radiated electric field intensity of EMP in all frequency bands enhances with the increase in discharge voltage or storage capacitance. Because of the polarization mismatch, the received field intensity in the ball-plate electrode configuration is the weakest compared to the plate-plate and ball-ball electrode. The whole radiation process of EMP from spark discharge plasma can be simulated by a combined dipole-loop antenna model well. The dipole antenna and loop antenna models are used to depict the radiation process of EMP during the discharge transient process and subsequently the energy releasing process, respectively. These results provide some fundamental knowledge for further study of RF EMP from gas discharge.
Experimental reconstruction of the contact resonance shape factor for quantification and amplification of bias-induced strain in atomic force microscopy
Authors: Killgore Jason P. , Deolia Akshay , Robins Lawrence , Murray Todd W.
Published: April 2019

The contact resonance (CR) of a surface coupled atomic force microscope (AFM) cantilever can act as an amplifier of AC surface motion for piezoresponse force microscopy and related methods. However, the amplifier properties of the CR vary depending on tip-sample boundary conditions, leading to the appearance of displacement amplitude contrast when only stiffness contrast exists. It was recently proposed that the shape of the vibrating cantilever as a function of CR frequency could be analytically modeled and a shape factor calibration could be applied. Here, we demonstrate an experimental reconstruction of the contact resonance shape factor that can be used to quantify surface displacements in AFM measurements, without reliance on analytical models with uncertain input parameters. We demonstrate accurate quantification of surface displacement in periodically poled lithium niobate and pave the way for quantification of extremely small surface strains in the future.
Kinetic effects in a plasma crystal induced by an external electron beam
Authors: Ticoş Cătălin M. , Ticoş Dorina , Williams Jeremiah D.
Published: April 2019

The kinetic effects on the dust particles are studied experimentally in a plasma crystal locally irradiated by a narrow pulsed electron beam with an energy of 13 keV and a peak current of 4 mA. We observe in the top layer of the plasma crystal the formation of a stable dust flow along the irradiation direction in the first ≈200 ms of the interaction. The dust flow eventually becomes perturbed later in time, with the dust particles having chaotic trajectories as they are still drifting in the beam direction. The speed of the dust flow is mapped in a horizontal plane using the particle image velocimetry technique (PIV). The kinetic energy of the flow and its vorticity are deduced based on the speed vectors provided by PIV. A maximum energy transfer factor ≈0.048 from the electron beam is inferred considering the peak kinetic energy (≈625 eV) of the dust flow. Vortices and tripolar vortices are observed when the dust flow becomes perturbed.
Mechanical properties of boron arsenide single crystal
Authors: Tian Fei , Luo Kun , Xie Chenlong , Liu Bing , Liang Xiaowei , Wang Linyan , Gamage Geethal Amila , Sun Haoran , Ziyaee Hamidreza , Sun Jingying , Zhao Zhisheng , Xu Bo , Gao Guoying , Zhou Xiang-Feng , Ren Zhifeng
Published: April 2019

As the only semiconductor material exhibiting ultrahigh thermal conductivity under ambient conditions, cubic boron arsenide (BAs) is currently attracting great interest. Thanks to the development of high-quality BAs single crystal growth techniques, investigation of its basic physical properties has now become possible. Here, the mechanical properties of BAs single crystals are studied by experimental measurements combined with first-principles calculations. A Vickers hardness of 22 GPa suggests that BAs is a hard material, although not among the hardest. The bulk and Young's moduli are measured to be 142 and 388 GPa, respectively. These important mechanical performance parameters, in conjunction with the unusual high thermal conductivity, show great potential for BAs to serve in next-generation semiconductor applications.
Light–heat conversion dynamics in highly diversified water-dispersed hydrophobic nanocrystal assemblies
Authors: Mazzanti Andrea , Yang Zhijie , Silva Mychel G. , Yang Nailiang , Rizza Giancarlo , Coulon Pierre-Eugène , Manzoni Cristian , de Paula Ana Maria , Cerullo Giulio , Della Valle Giuseppe , Pileni Marie-Paule
Published: April 2019

Significance

Metal and semiconductor nanoparticles have been widely exploited in research, because of their striking capability to concentrate light energy at the nanoscale and convert it to heat at ultrahigh speed. However, most nanoparticles are made of homogeneous materials, which limits the possibility to engineer their photothermal properties. Additional degrees of freedom are provided by nanoassemblies: periodically arranged nanocrystals of few nanometers in size embedded into an organic matrix. Here we display a specific mechanism presiding over the light–heat ultrafast conversion in a highly diversified family of nanoassemblies, which is intimately related to their hybrid composition at the nanoscale. The exceptional photothermal properties of nanocrystal assemblies open prospects in nanomedicine (photothermal therapy) and energy harvesting.
Realizing the values of natural capital for inclusive, sustainable development: Informing China’s new ecological development strategy
Authors: Zheng Hua , Wang Lijuan , Peng Wenjia , Zhang Cuiping , Li Cong , Robinson Brian E. , Wu Xiaochen , Kong Lingqiao , Li Ruonan , Xiao Yi , Xu Weihua , Ouyang Zhiyun , Daily Gretchen C.
Published: April 2019

Significance

Achieving inclusive, green development is crucial to China and the world. Over the past century, great increases in agricultural production have been achieved at the expense of other ecosystem benefits, such as flood control, water purification, climate stabilization, and biodiversity conservation. We report on an application of China’s new “Ecological Development Strategy,” which aims to break these trade-offs and be scaled nationwide. Focusing on Hainan Island, where rubber production has driven loss of natural forest, we identified a two-pronged strategy that would eliminate these trade-offs, simultaneously diversifying and enhancing product provision, rural incomes, and many other ecosystem benefits. This win−win approach has broad applicability in the plantation regions in China, across South and Southeast Asia, and beyond.
Superhydrophobic frictions
Authors: Mouterde Timothée , Raux Pascal S. , Clanet Christophe , Quéré David
Published: April 2019

Significance

The matchless mobility of water on superhydrophobic materials is often considered as the hallmark of water repellency. The friction of drops is indeed found to be unusual: instead of observing classical friction such as due to contact line and liquid viscosity, we show that the main source of resistance to the water motion arises from the air around it. This explains why the drop velocity becomes quasi-independent of its viscosity at low viscosity and more generally why the mobility is so high. We also discuss the case of more viscous liquids whose rolling motion induces a bulk viscous dissipation that caps the mobility.
Translingual quoting in journalism
Authors: Haapanen Lauri , Perrin Daniel
Published: April 2019

This chapter focuses on translingual quoting (TQ), i.e. the sub-process of news-writing by which utterances from sources are both quoted and translated. Analyses of journalists’ mental and material activities suggest conceptualizing TQ as a complex and dynamic activity in which journalists’ individual and collective (e.g. institutional) language awareness, knowledge, and practices interact with multi-layered contexts of text production. Based on this empirically and theoretically grounded concept of TQ, the chapter presents a two-part typology of TQ: in sequential TQ, ready-made media items or interview materials are translated into another language; in parallel TQ, interviews and/or texts for media items are produced in different languages by one and the same journalist.
News translation on the Canadian Broadcasting Corporation’s English and French websites
Authors: Gendron Philippe , Conway Kyle , Davier Lucile
Published: April 2019

This chapter examines the techniques journalists use to incorporate translated speech into news stories published on the websites of the French and English networks of the Canadian Broadcasting Corporation. It examines four sets of stories: national political news in French (76 stories) and in English (63 stories) and local news from Canada’s capital region in French (85 stories) and in English (98 stories). It combines content analysis, textual analysis, and ethnography to provide an update of past research about the Corporation’s television news programs in the early 1990s. It reveals that the asymmetries that have long shaped the Corporation’s French- and English-language news continue to operate, although in different form, and they continue to influence the ways journalists incorporate translated speech into their stories.
Technological convergence threatening translation
Authors: Davier Lucile
Published: April 2019

Le Droit is a monolingual French-language regional newspaper targeting audiences in two Canadian provinces. Although its multimodal content appears to be in French only, English permeates the daily work of reporters. Data include sessions of observation, semi-structured interviews, and text collection on different platforms (print, website, applications, and social media). This chapter shows that, at the level of news-gathering, contacts with English sources seem partially unavoidable or even desirable. At the level of production, however, all traces of translation are erased in the written form, while French voices are systematically preferred in audiovisual content. The growing importance of audiovisual content seems to predict the exclusion of sources in a second language.
Sensory Linguistics
Authors: Winter Bodo
Published: April 2019

One of the most fundamental capacities of language is the ability to express what speakers see, hear, feel, taste, and smell. Sensory Linguistics is the interdisciplinary study of how language relates to the senses. This book deals with such foundational questions as: Which semiotic strategies do speakers use to express sensory perceptions? Which perceptions are easier to encode and which are “ineffable”? And what are appropriate methods for studying the sensory aspects of linguistics? After a broad overview of the field, a detailed quantitative corpus-based study of English sensory adjectives and their metaphorical uses is presented. This analysis calls age-old ideas into question, such as the idea that the use of perceptual metaphors is governed by a cognitively motivated “hierarchy of the senses”. Besides making theoretical contributions to cognitive linguistics, this research monograph showcases new empirical methods for studying lexical semantics using contemporary statistical methods.
/h/ insertion as a ‘camouflage archaism’?
Authors: Schreier Daniel
Published: April 2019

This article documents the historical development and synchronic variation of so-called “/h/ insertion” (/h/ before vowel-initial words such asapple,under, etc.). It argues that the maintenance of /h/ insertion in post-colonial English varieties around the world provides an ideal opportunity for research on language change under dialect contact scenarios involving British donors and other dialects. After an assessment of regional distribution patterns in current World Englishes, I present some first findings from a large-scale quantitative analysis of Tristan da Cunha English, where /h/ insertion, firmly attested yet nearing obsolescence in British English, has survived into the 21st century. The quantitative analysis provides important insights into donor attribution and competition-selection processes that accompany dialect contact and koinéization, with special reference to theoretical concepts such as colonial lag, feature pool formation and founder effects. A holistic application of the concept of colonial lag to post-colonial English varieties needs to be refined and critically assessed. I argue that entire linguistic systems (in the form of koinés) are not conservative as such but that arrested language (and dialect) change operates on a feature-specific level instead.
Variability within varieties of English
Authors: Oetting Janna B.
Published: April 2019

In this article, I present findings from studies completed with children who speak nonmainstream dialects of English, including African American English as spoken in LA, MI, and the Gullah/Geechee Corridor of SC and Southern White English as spoken in rural LA by children with and without Cajun influence. Using these studies, I describe some of the ways in which typically developing child speakers of various nonmainstream dialects differ from each other and some of the ways in which nonmainstream English-speaking children with specific language impairment differ from their same dialect-speaking, typically developing peers. I conclude that profiles of typicality and impairment are not the same – the latter contributes a more restricted range of variation than the former.
Elements of syntax
Authors: van Riemsdijk Henk
Published: April 2019

This contribution presents a somewhat autobiographical overview of the author’s struggle in coming to grips with the undeniable central role that the forces of attraction and repulsion play in the grammar of natural languages. It is therefore a tale of good and bad ideas, where the bad ideas sometimes suppressed the good ones. After disentangling these previous attempts at a more or less comprehensive theory of repulsion and attraction, I present a sketchy research program for where I think we need to go to find a satisfactory solution.
Preliminaries to delicate matters
Authors: Lim Ni-Eng
Published: April 2019

The meta-language unit “I say to you” is frequently heard in Mandarin Chinese conversations, and are most commonly expressed as wo gen ni shuo ‘I say to you’, wo gen ni jiang ‘I talk to you’, or wo gaosu ni ‘I tell you’, collectively termed “I-say-to-you” expressions. Quantitative investigations reveal that they are dedicated interactional resources found only in spoken conversation. By using conversation analytic methodology, further examination of their sequential trajectory shows that a core function of “I-say-to-you” expressions is to preface upcoming “delicate” matters, such as dispreferred next action, disagreement or disaffiliative turn, and other actions that may be resistance-implicative for the recipient. As a preface, “I-say-to-you” expressions can be used by the speaker to secure multi-turns space with which to gradually deliver the “delicate” matter and achieve other interactional goals.
MiR-125b regulates the proliferation and metastasis of triple negative breast cancer cells via the Wnt/β-catenin pathway and EMT
Authors: Nie Jun , Jiang Hong-Chao , Zhou Yong-Chun , Jiang Bo , He Wen-Jie , Wang Yu-Feng , Dong Jian
Published: April 2019

Background/aim: MiR-125b plays an important role in breast cancer. The current study was to explore the expression and function of miR-125b in triple negative breast cancer cells. Materials and methods: The expression of miR-125b in human TNBC samples and cell lines were examined by qRT-PCR. MTT, scratch assays and transwell assays were utilized to observe the proliferation, migration and invasion ability. MiR-125b’s target gene and downstream signaling pathways were investigated by Luciferase Reporter Assays, qRT-PCR, immunofluorescence assays and western bolt. Results: MiR-125b was highly expressed in human TNBC tissues and cell lines. Inhibiting miR-125b expression suppressed the proliferation, cell migration and invasion. The three-prime untranslated region (3´-UTR) of adenomatous polyposis coli (APC) mRNA contains miR-125b binding sites, and inhibiting miR-125b expression suppressed the activity of the intracellular Wnt/β-catenin pathways and EMT. Conclusion: Inhibiting miR-125b regulates the Wnt/β-catenin pathway and EMT to suppress the proliferation and migration of MDA-MB-468 TNBC cells.
Learner agency and the curriculum: a critical realist perspective
Authors: Manyukhina Yana , Wyse Dominic
Published: April 2019

Agency, understood as the capacity to act independently and to make one's own choices, is considered central to children's development. Thus, education, and hence education curricula, have a role in the development of learner agency. While curriculum development is a key focus for educational theory, research, policy, and classroom practice, the potential implications of curriculum content selections for learner agency remain underexplored. Theoretically, this paper engages with critical realism, explaining how it can provide theoretical foundation for a more comprehensive view of learner agency and, by implication, more balanced curricula. Empirically, the paper draws on the findings from a content analysis of the national curriculum documents of four countries with relatively high scores in international comparative tables, England, Australia, Hong‐Kong, and Canada, to develop a new typology of primary curricula. Based on the extent of emphasis placed on knowledge versus skills, values, and attitudes, three types of curricula were identified: knowledge‐based, skills‐oriented, and learner‐centred. Due to its significant theoretical and practical influence globally, we focus on the knowledge‐based model and its likely impact on students’ agency. We conclude by highlighting the importance of making learner agency a key orientation of the curriculum and suggesting directions for future research.
PARTY POLITICS IN PORTUGAL
Authors: Antónia Pires de Almeida Maria
Published: April 2019

Since the Portuguese revolution of April 25th, 1974, and the beginning of the democratic regime (with the first elections for parliament held on April 25th, 1975), political parties dominate the electoral process, both on central government and on the municipalities. The analysis of the political elites, their party filiations and recruitment and their social backgrounds has occupied Portuguese social scientists for the last years. With this paper, the author proposes to establish the relationship between these two levels of government, national and local, and access the importance of political parties in each of them. Many mayors’ political careers include vertical mobility, both upwards and downwards: from mayors to members of parliament to members of the European Parliament and ministers or even Prime Minister and President of the Republic (in the case of two mayors of Lisbon), or from ministers and members of parliament to mayors. In all of these cases, their party and their position within the party has played a central role, even when some individuals have pursued other party choices in order to get re-elected, or even have presented independent candidacies (only possible since 1997).
Contact homology and virtual fundamental cycles
Authors: Pardon John
Published: April 2019

We give a construction of contact homology in the sense of Eliashberg–Givental–Hofer. Specifically, we construct coherent virtual fundamental cycles on the relevant compactified moduli spaces of pseudo-holomorphic curves.
HiCNN: a very deep convolutional neural network to better enhance the resolution of Hi-C data
Authors: Liu Tong , Wang Zheng
Published: April 2019

Motivation

High-resolution Hi-C data are indispensable for the studies of three-dimensional (3D) genome organization at kilobase level. However, generating high-resolution Hi-C data (e.g. 5 kb) by conducting Hi-C experiments needs millions of mammalian cells, which may eventually generate billions of paired-end reads with a high sequencing cost. Therefore, it will be important and helpful if we can enhance the resolutions of Hi-C data by computational methods.

Results

We developed a new computational method named HiCNN that used a 54-layer very deep convolutional neural network to enhance the resolutions of Hi-C data. The network contains both global and local residual learning with multiple speedup techniques included resulting in fast convergence. We used mean squared errors and Pearson’s correlation coefficients between real high-resolution and computationally predicted high-resolution Hi-C data to evaluate the method. The evaluation results show that HiCNN consistently outperforms HiCPlus, the only existing tool in the literature, when training and testing data are extracted from the same cell type (i.e. GM12878) and from two different cell types in the same or different species (i.e. GM12878 as training with K562 as testing, and GM12878 as training with CH12-LX as testing). We further found that the HiCNN-enhanced high-resolution Hi-C data are more consistent with real experimental high-resolution Hi-C data than HiCPlus-enhanced data in terms of indicating statistically significant interactions. Moreover, HiCNN can efficiently enhance low-resolution Hi-C data, which eventually helps recover two chromatin loops that were confirmed by 3D-FISH.

Availability and implementation

HiCNN is freely available at http://dna.cs.miami.edu/HiCNN/.

Supplementary information

Supplementary data are available at Bioinformatics online.
β-hCG-induced mutant BRCA1 ignites drug resistance in susceptible breast tissue
Authors: Sengodan Satheesh Kumar , Hemalatha Sreelatha K , Nadhan Revathy , Somanathan Thara , Mathew Arun Peter , Chil Arkadiusz , Kopczynski Janusz , Nair Rakesh Sathish , Kumar Jerald Mahesh , Srinivas Priya
Published: April 2019

β-hCG expression in breast cancer is highly controversial with reports supporting both protective and tumorigenic effects. It has also been reported that risk of breast cancer at an early age is increased with full-term pregnancies if a woman is a BRCA1 mutation carrier. We have already demonstrated that BRCA1-defective cells express high levels of β-hCG and that when BRCA1 is restored, β-hCG level is reduced. Also, BRCA1 can bind to the promoter and reduce the levels of β-hCG. β-hCG induces tumorigenicity in BRCA1-defective cells by directly binding to TGFBRII and induces TGFBRII-mediated cell proliferation. In this study, we analyzed the mechanism of action of β-hCG on BRCA1 expression and its influence on drug sensitivity in breast cancer cells. We demonstrate that β-hCG induces mutant BRCA1 protein expression in BRCA1 mutant cells; however, in BRCA1 wild-type cells, β-hCG reduced wild-type BRCA1 protein expression. Transcriptionally, β-hCG could induce Slug/LSD1-mediated repression of wild-type and mutant BRCA1 messenger RNA levels. However, β-hCG induces HSP90-mediated stabilization of mutant BRCA1 and hence the overexpression of mutant BRCA1 protein, resulting in partial restoration of homologous recombination repair of damaged DNA. This contributes to drug resistance to HSP90 inhibitor 17AAG in BRCA1-defective cancer cells. A combination of HSP90 inhibitor and TGFBRII inhibitor has shown to sensitize β-hCG expressing BRCA1-defective breast cancers to cell death. Targeting the β-hCG–HSP90–TGFBRII axis could prove an effective treatment strategy for BRCA1-mutated breast tumors.
Clinical and angiographic outcomes of bioabsorbable vs. permanent polymer drug-eluting stents in Sweden: a report from the Swedish Coronary and Angioplasty Registry (SCAAR)
Authors: Buccheri Sergio , James Stefan , Lindholm Daniel , Fröbert Ole , Olivecrona Göran K , Persson Jonas , Hambraeus Kristina , Witt Nils , Erlinge David , Angerås Oskar , Lagerqvist Bo , Sarno Giovanna
Published: April 2019

Aims

Randomized clinical trials have consistently demonstrated the non-inferiority of bioabsorbable polymer drug-eluting stents (BP-DES) with respect to DES having permanent polymers (PP-DES). To date, the comparative performance of BP- and PP-DES in the real world has not been extensively investigated.

Methods and results

From October 2011 to June 2016, we analysed the outcomes associated with newer generation DES use in Sweden. After stratification according to the type of DES received at the index procedure, a total of 16 504 and 79 106 stents were included in the BP- and PP-DES groups, respectively. The Kaplan–Meier estimates for restenosis at 2 years were 1.2% and 1.4% in BP- and PP-DES groups, respectively. Definite stent thrombosis (ST) was low in both groups (0.5% and 0.7% in BP- and PP-DES groups, respectively). The adjusted hazard ratio (HR) for either restenosis or definite ST did not differ between BP- and PP-DES [adjusted HR 0.95, 95% confidence interval (CI) 0.74–1.21; P = 0.670 and adjusted HR 0.79, 95% CI 0.57–1.09; P = 0.151, respectively]. Similarly, there were no differences in the adjusted risk of all-cause death and myocardial infarction (MI) between the two groups (adjusted HR for all-cause death 1.01, 95% CI 0.82–1.25; P = 0.918 and adjusted HR for MI 1.05, 95% CI 0.93–1.19; P = 0.404).

Conclusion

In a large, nationwide, and unselected cohort of patients, percutaneous coronary intervention with BP-DES implantation was not associated with an incremental clinical benefit over PP-DES use at 2 years follow-up.
Islands in the stream: from individual to communal fiber degradation in the rumen ecosystem
Authors: Moraïs Sarah , Mizrahi Itzhak
Published: April 2019

The herbivore rumen ecosystem constitutes an extremely efficient degradation machinery for the intricate chemical structure of fiber biomass, thus, enabling the hosting animal to digest its feed. The challenging task of deconstructing and metabolizing fiber is performed by microorganisms inhabiting the rumen. Since most of the ingested feed is comprised of plant fiber, these fiber-degrading microorganisms are of cardinal importance to the ecology of the rumen microbial community and to the hosting animal, and have a great impact on our environment and food sustainability. We summarize herein the enzymological fundamentals of fiber degradation, how the genes encoding these enzymes are spread across fiber-degrading microbes, and these microbes' interactions with other members of the rumen microbial community and potential effect on community structure. An understanding of these concepts has applied value for agriculture and our environment, and will also contribute to a better understanding of microbial ecology and evolution in anaerobic ecosystems.
Revisiting gametocyte biology in malaria parasites
Authors: Ngotho Priscilla , Soares Alexandra Blancke , Hentzschel Franziska , Achcar Fiona , Bertuccini Lucia , Marti Matthias
Published: April 2019

Gametocytes are the only form of the malaria parasite that is transmissible to the mosquito vector. They are present at low levels in blood circulation and significant knowledge gaps exist in their biology. Recent reductions in the global malaria burden have brought the possibility of elimination and eradication, with renewed focus on malaria transmission biology as a basis for interventions. This review discusses recent insights into gametocyte biology in the major human malaria parasite, Plasmodium falciparum and related species.
Trauma, Memory and the Act of Writing in Ruth Klüger’s Autobiographical Project
Authors: Painitz Sarah
Published: April 2019

This essay intends to shed light on the motivation behind Ruth Klüger’s autobiographical project by examining the relationship between trauma, memory and the act of writing. Exploring the catalyst for writing reveals that Klüger’s autobiographical texts have a dual function: they serve as a public call for dialogue, as well as a kind of therapy allowing her to work through the traumas of her past. I demonstrate that for this reason, it is crucial to take into consideration not just the well-known weiter leben: Eine Jugend (1992), but also its revised English self-translation Still Alive: A Holocaust Girlhood Remembered (2001). Writing, editing, revising and translating create a space for Klüger’s continuous engagement with her past and its traumas – an engagement that is ongoing, continuing beyond the first writing of the text, and that stems from an innate desire to understand better the driving forces of her own life and her survival against all odds.
Non-convex low-rank matrix recovery with arbitrary outliers via median-truncated gradient descent
Authors: Li Yuanxin , Chi Yuejie , Zhang Huishuai , Liang Yingbin
Published: April 2019

Recent work has demonstrated the effectiveness of gradient descent for directly recovering the factors of low-rank matrices from random linear measurements in a globally convergent manner when initialized properly. However, the performance of existing algorithms is highly sensitive in the presence of outliers that may take arbitrary values. In this paper, we propose a truncated gradient descent algorithm to improve the robustness against outliers, where the truncation is performed to rule out the contributions of samples that deviate significantly from the sample median of measurement residuals adaptively in each iteration. We demonstrate that, when initialized in a basin of attraction close to the ground truth, the proposed algorithm converges to the ground truth at a linear rate for the Gaussian measurement model with a near-optimal number of measurements, even when a constant fraction of the measurements are arbitrarily corrupted. In addition, we propose a new truncated spectral method that ensures an initialization in the basin of attraction at slightly higher requirements. We finally provide numerical experiments to validate the superior performance of the proposed approach.
Association of the quality of antenatal care with neonatal mortality: meta-analysis of individual participant data from 60 low- and middle-income countries
Authors: Neupane Subas , Doku David Teye
Published: April 2019

Background

We investigated the quality of antenatal care (ANC) and its effect on neonatal mortality in 60 low- and middle-income countries (LMICs).

Methods

We used pooled comparable cross-sectional surveys from 60 LMICs (n=651 681). Cox proportional hazards multivariable regression models and meta-regression analysis were used to assess the effect of the quality of ANC on the risk of neonatal mortality. Kaplan–Meier survival curves were used to describe the time-to-event patterns of neonatal survival in each region.

Results

Pooled estimates from meta-analysis showed a 34% lower risk of neonatal mortality for children of women who were attended to at ANC by skilled personnel. Sufficient ANC advice lowered the risk of neonatal mortality by 20%. Similarly, children of women who had adequate ANC had a 39% lower risk of neonatal mortality. The pooled multivariable model showed an association of neonatal mortality with the ANC quality index (HR 0.85, 95% CI 0.77 to 0.93).

Conclusions

Improvement in the quality of ANC can reduce the risk of neonatal mortality substantially. Pursuing sustainable development goal 3, which aims to reduce neonatal mortality to 12 per 1000 live births by 2030, should improve the quality of ANC women receive in LMICs.
Differences in Mosquito Communities in Six Cities in Oklahoma
Authors: Bradt David , Wormington Jillian D , Long James M , Hoback W Wyatt , Noden Bruce H
Published: April 2019

Vector-borne diseases in the United States have recently increased as a result of the changing nature of vectors, hosts, reservoirs, pathogens, and the ecological and environmental conditions. Current information on vector habitats and how mosquito community composition varies across space and time is vital to successful vector-borne disease management. This study characterizes mosquito communities in urban areas of Oklahoma, United States, an ecologically diverse region in the southern Great Plains. Between May and September 2016, 11,996 female mosquitoes of 34 species were collected over 798 trap nights using three different trap types in six Oklahoma cities. The most abundant species trapped were Culex pipiens L. complex (32.4%) and Aedes albopictus (Skuse) (Diptera: Culicidae) (12.0%). Significant differences among mosquito communities were detected using analysis of similarities (ANOSIM) between the early (May–July) and late (August–September) season. Canonical correlation analysis (CCA) further highlighted the cities of Altus and Idabel as relatively unique mosquito communities, mostly due to the presence of Aedes aegypti (L.) and salt-marsh species and absence of Aedes triseriatus (Say) in Altus and an abundance of Ae. albopictus in Idabel. These data underscore the importance of assessing mosquito communities in urban environments found in multiple ecoregions of Oklahoma to allow customized vector management targeting the unique assemblage of species found in each city.
TP53 Status as a Determinant of Pro- vs Anti-Tumorigenic Effects of Estrogen Receptor-Beta in Breast Cancer
Authors: Mukhopadhyay Utpal K , Oturkar Chetan C , Adams Christina , Wickramasekera Nadi , Bansal Sanjay , Medisetty Rajesh , Miller Austin , Swetzig Wendy M , Silwal-Pandit Laxmi , Børresen-Dale Anne-Lise , Creighton Chad J , Park Jun Hyoung , Konduri Santhi D , Mukhopadhyay Alka , Caradori Alexander , Omilian Angela , Bshara Wiam , Kaipparettu Benny Abraham , Das Gokul M
Published: April 2019

Background

Anti-tumorigenic vs pro-tumorigenic roles of estrogen receptor-beta (ESR2) in breast cancer remain unsettled. We investigated the potential of TP53 status to be a determinant of the bi-faceted role of ESR2 and associated therapeutic implications for triple negative breast cancer (TNBC).

Methods

ESR2-TP53 interaction was analyzed with multiple assays including the in situ proximity ligation assay. Transcriptional effects on TP53-target genes and cell proliferation in response to knocking down or overexpressing ESR2 were determined. Patient survival according to ESR2 expression levels and TP53 mutation status was analyzed in the basal-like TNBC subgroup in the Molecular Taxonomy of Breast Cancer International Consortium (n = 308) and Roswell Park Comprehensive Cancer Center (n = 46) patient cohorts by univariate Cox regression and log-rank test. All statistical tests are two-sided.

Results

ESR2 interaction with wild-type and mutant TP53 caused pro-proliferative and anti-proliferative effects, respectively. Depleting ESR2 in cells expressing wild-type TP53 resulted in increased expression of TP53-target genes CDKN1A (control group mean [SD] = 1 [0.13] vs ESR2 depletion group mean [SD] = 2.08 [0.24], P = .003) and BBC3 (control group mean [SD] = 1 [0.06] vs ESR2 depleted group mean [SD] = 1.92 [0.25], P = .003); however, expression of CDKN1A (control group mean [SD] = 1 [0.21] vs ESR2 depleted group mean [SD] = 0.56 [0.12], P = .02) and BBC3 (control group mean [SD] = 1 [0.03] vs ESR2 depleted group mean [SD] = 0.55 [0.09], P = .008) was decreased in cells expressing mutant TP53. Overexpressing ESR2 had opposite effects. Tamoxifen increased ESR2-mutant TP53 interaction, leading to reactivation of TP73 and apoptosis. High levels of ESR2 expression in mutant TP53-expressing basal-like tumors is associated with better prognosis (Molecular Taxonomy of Breast Cancer International Consortium cohort: log-rank P = .001; hazard ratio = 0.26, 95% confidence interval = 0.08 to 0.84, univariate Cox P = .02).

Conclusions

TP53 status is a determinant of the functional duality of ESR2. Our study suggests that ESR2-mutant TP53 combination prognosticates survival in TNBC revealing a novel strategy to stratify TNBC for therapeutic intervention potentially by repurposing tamoxifen.
Emerging mould infections: Get prepared to meet unexpected fungi in your patient
Authors: Dellière Sarah , Rivero-Menendez Olga , Gautier Cécile , Garcia-Hermoso Dea , Alastruey-Izquierdo Ana , Alanio Alexandre
Published: April 2019

Invasive fungal diseases are increasing issues in modern medicine, where the human immunodeficiency virus (HIV) pandemic and the wider use of immunosuppressive drugs generate an ever-growing number of immunocompromised patients with an increased susceptibility to uncommon fungal pathogens. In the past decade, new species have been reported as being responsible for disseminated and invasive fungal diseases in humans. Among them, the following genera are rare but seem emerging issues: Scopulariopsis, Hormographiella, Emergomyces, Westerdykella, Trametes, Actinomucor, Saksenaea, Apophysomyces, and Rhytidhysteron. Delay in diagnosis, which is often the case in these infections, jeopardizes patients’ prognosis and leads to increased mortality. Here we summarize the clinical and biological presentation and the key features to identify these emerging pathogens and we discuss the available antifungal classes to treat them. We focused on Pubmed to recover extensively reported human invasive cases and articles regarding the nine previously cited fungal organisms. Information concerning patient background, macroscopic and microscopic description and pictures of these fungal organisms, histological features in tissues, findings with commonly used antigen tests in practice, and hints on potential efficient antifungal classes were gathered. This review's purpose is to help clinical microbiologists and physicians to suspect, identify, diagnose, and treat newly encountered fungi in hospital settings.