bluuebunny/crossref_metadata_2025 huggingface dataset:
A molecular network for functional versatility of HECATE transcription factors
Authors: Gaillochet Christophe , Jamge Suraj , van der Wal Froukje , Angenent Gerco , Immink Richard , Lohmann Jan U.
Published: April 2018

During the plant life cycle, diverse signaling inputs are continuously integrated and engage specific genetic programs depending on the cellular or developmental context. Consistent with an important role in this process, HECATE (HEC) basic helix–loop–helix transcription factors display diverse functions, from photomorphogenesis to the control of shoot meristem dynamics and gynoecium patterning. However, the molecular mechanisms underlying their functional versatility and the deployment of specific HEC subprograms remain elusive. To address this issue, we systematically identified proteins with the capacity to interact with HEC1, the best‐characterized member of the family, and integrated this information with our data set of direct HEC1 target genes. The resulting core genetic modules were consistent with specific developmental functions of HEC1, including its described activities in light signaling, gynoecium development and auxin homeostasis. Importantly, we found that HEC genes also play a role in the modulation of flowering time, and uncovered that their role in gynoecium development may involve the direct transcriptional regulation of NGATHA1 (NGA1) and NGA2 genes. NGA factors were previously shown to contribute to fruit development, but our data now show that they also modulate stem cell homeostasis in the shoot apical meristem. Taken together, our results delineate a molecular network underlying the functional versatility of HEC transcription factors. Our analyses have not only allowed us to identify relevant target genes controlling shoot stem cell activity and a so far undescribed biological function of HEC1, but also provide a rich resource for the mechanistic elucidation of further context‐dependent HEC activities.
Unpacking research and practice in world Englishes and Second Language Acquisition
Authors: Kubota Ryuko
Published: April 2018

Research on world Englishes and Second Language Acquisition has conceptualized language, language users, and language learning as diverse and dynamic, broadening conventional knowledge. Yet, research outputs have not influenced language education policies in Expanding Circle countries, which favor Inner Circle standardized English, promote teaching English to young learners, and require monolingual teaching of English, as seen in the case of Japanese primary and secondary education. These activities are perpetuated by macro‐level language ideology and broader political, historical, and economic forces including neoliberalism that exist at a super macro level. Examining the roots of these practices directs our attention to both macro and super‐macro issues as well as to complicities between research/researchers and broader ideological and structural issues. Recommendations are offered to invite researchers to begin exploring how research can make impacts on real‐world issues.
Coda 1 World Englishes and Second Language Acquisition: Working towards a common goal
Authors: Gass Susan
Published: April 2018

Although some have argued that world Englishes and Second Language Acquisition are in a relationship of conflict, my own view is that this is not necessarily the case. Indeed, it is possible to argue that the relationship between the two paradigms is better characterized as ‘benign neglect’ rather than that of conflict. Both fields, I would suggest, might benefit from truly collaborative research and scholarship, but such collaboration does not necessarily come easily, as researchers typically have expertise in one field rather than another, and this can frequently lead to miscommunication and misunderstanding, however well‐intentioned potential collaborators might be. From the point of view of SLA, one might also question the heavy emphasis on ‘Englishes’ in this context, and I end this coda with a discussion of the writing of Lahiri (2016), whose written account of the learning of Italian illustrates the interconnection of both cognitive and social factors in second language development.
Coda 2 A bridge half‐built: Toward a holistic theory of Second Language Acquisition and world Englishes
Authors: Sridhar S.N. , Sridhar Kamal K.
Published: April 2018

In the concluding contribution to this special issue, we return to the key issue that motivated our 1986 article on world Englishes (WE) and Second Language Acquisition (SLA). This coda begins by considering the impact of WE on SLA at a number of levels, with reference to the pluricentricity of English, conceptions of the ‘native speaker’, formalist ontology, functional perspectives, multilingualism, and other dynamic approaches to SLA. We then proceed to consider recent critiques of the WE paradigm, before moving to a discussion of the current synergy between world Englishes and Second Language Acquisition studies, noting that in many contemporary approaches to SLA, ‘the monolingual bias has given way to a multilingual turn.’ Nevertheless, even if there is a far greater appreciation of world Englishes than three decades ago, it is still evidently the case that textbooks in Second Language Acquisition continue to be focused on cognitive and structural dimensions of language acquisition, and often fail to incorporate social, functional and multilingual perspectives.
Band-Gap Properties of Elastic Metamaterials With Inerter-Based Dynamic Vibration Absorbers
Authors: Fang Xiang , Chuang Kuo-Chih , Jin Xiaoling , Huang Zhilong
Published: April 2018

In this paper, inerter-based dynamic vibration absorbers (IDVAs) are applied in elastic metamaterials to broaden low-frequency band gaps. A discrete mass-spring lattice system and a distributed metamaterial beam carrying a periodic array of IDVAs are, respectively, considered. The IDVA consists of a spring and an inerter connected to a traditional mass-spring resonator. Compared to the traditional resonators, the special designed IDVAs generate two local-resonance (LR) band gaps for the discrete lattice system, a narrow low-frequency band gap and a wider high-frequency one. For the distributed IDVA-based metamaterial beam, in addition to the generated two separated LR band gaps, the Bragg band gap can also be significantly broadened and the three band gaps are very close to each other. Being able to amplify inertia, the IDVAs can be relatively light even operated for opening up low-frequency band gaps. When further introducing a dissipative damping mechanism into the IDVA-based metamaterials, the two close-split LR band gaps in the lattice system are merged into one wide band gap. As for the metamaterial beam with the dissipative IDVAs, an even wider band gap can be acquired due to the overlap of the adjacent LR and Bragg-scattering band gaps.
Comparative study between four ultrasound Shear Waves Elastographic methods for liver fibrosis assessment
Authors: Sporea Ioan , Mare Ruxandra , Lupusoru Raluca , Popescu Alina , Danila Mirela , Bende Felix , Sirli Roxana
Published: April 2018

Aims: Non-invasive methods to assess the severity of chronic liver diseases have become more and more popular. The aim of our study was to evaluate the correlation of four Shear Waves Elastographic methods in a cohort of patients with chronic liver diseases of mixed etiologies and to compare their performances for liver fibrosis evaluation.Material and methods: A prospective study was conducted on 127 consecutive patients with chronic liver diseases of mixed etiologies. LS measurements were performed in all subjects, in one session, during the same day, by means of 4 elastographic methods: Transient Elastography (TE), Virtual Touch Quantification (VTQ), ElastPQ and 2D-SWE.SSI. The diagnosis accuracies of VTQ, ElastPQ, 2D-SWE.SSI were then compared using TE as reference method.Results: Valid LS measurements by all four shear waves ultrasound elastographic methods were obtained in 116/127 subjects with VTQ, in 108/127 subjects with 2D-SWE.SSI, in 111/127 with TE and in 109/127 with ElastPQ, so the final analysis included 82/127 subjects (64.5%). A good and significant correlation was found between all 4 elastographic methods. The diagnostic accuracy of VTQ, 2D-SWE.SSI and ElastPQ for the diagnosis of significant and severe fibrosis (F2/F3), and liver cirrhosis were similar for all elastographic techniques: VTQ vs 2D-SWE.SSI vs ElastPQ: 84.1% vs 85.3% vs. 84% (p>0.05); 93.9% vs 94% vs 94% (p>0.05).Conclusion: considering TE as the reference method for liver fibrosis evaluation, VTQ, ElastPQ, and 2D-SWE.SSI obtained similar accuracies for diagnosing at least significant fibrosis (F≥2) and liver cirrhosis.
Baseball Physics: A New Mechanics Lab
Authors: Wagoner Kasey , Flanagan Daniel
Published: April 2018

The game of baseball provides an interesting laboratory for experimenting with mechanical phenomena (there are many good examples in The Physics Teacher, available on Professor Alan Nathan’s website, and discussed in Physics of Baseball & Softball). We have developed a lab, for an introductory-level physics course, that investigates many of these phenomena. The lab uses inexpensive, readily available equipment such as wooden baseball bats, baseballs, and actual Major League Baseball data. By the end of the lab, students have revisited many concepts they learned earlier in the semester and come away with an understanding of how to put seemingly disparate ideas together to analyze a fun sport.
Burst mode composite photography for dynamic physics demonstrations
Authors: Lincoln James
Published: April 2018

I am writing this article to raise awareness of burst mode photography as a fun and engaging way for teachers and students to experience physics demonstration activities. In the context of digital photography, “burst mode” means taking multiple photographs per second, and this is a feature that now comes standard on most digital cameras—including the iPhone. Sometimes the images are composited to imply motion from a series of still pictures. By analyzing the time between the photos, students can measure rates of velocity and acceleration of moving objects. Some of these composite photographs have already shown up in the AAPT High School Physics Photo Contest. In this article I discuss some ideas for using burst mode photography in the iPhone and provide a discussion of how to edit these photographs to create a composite image. I also compare the capabilities of the iPhone and GoPro cameras in creating these photographic composites.
Type of activity and order of experimental conditions affect noise annoyance by identifiable and unidentifiable transportation noise
Authors: White Kim , Bronkhorst Adelbert W. , Meeter Martijn
Published: April 2018

Previous studies have shown that identifiability of sound sources influence noise annoyance levels. The aim of the present experiment was to additionally study the effects of actively performing a task versus a less active pastime on noise annoyance. This was done by asking participants to perform a task (task condition) or read a magazine of their choice (no-task condition), while listening to identifiable and unidentifiable samples of transportation noise at varying sound exposure levels (55−85 ASEL). Annoyance was higher for identifiable samples (recordings) than for unidentifiable transformed samples (with equal spectral energy and envelope). Although there was no main effect of activity type on noise annoyance, for the transformed samples, an interaction was found between activity type and sound exposure levels: annoyance started lower in the no-task condition, but rose more steeply with ascending exposure levels than was the case during task performance (large effect). When assessing order effects, it was found that annoyance was higher when the task condition came first, especially for lower sound exposure levels (large effects). It is therefore concluded that the type of activity and the condition order do influence noise annoyance but in interaction with exposure levels, the type of noise and habituation.
Diffusion: How new research and data formats can be of use in simulations
Authors: Sauro Ronald
Published: April 2018

We will explore the new ways of measuring diffusion using free field methods and how those resulting data formats can be used in simulation programs such as EASE etc. This includes the calculation of complex balloons that reflect the total directivity of entire arrays of both diffractive and geometric styles of “diffusors.“ We will show actual measurements vs simulations. Included will be research done by Ron Sauro and extensions done by Jim DeGrandis that include some new graphs that extend our usage of phase data in an understanding of the psychoacoustic behavior of the human brain and our perception of how much data is of use to our designs.
The effects of frequency fine-tuning in hearing impaired phone recognition
Authors: Abavisani Ali , Allen Jont
Published: April 2018

A key factor on correct phone recognition in Normal Hearing (NH) and Hearing Impaired (HI) listeners, is the intensity of primary cue. One can assess this intensity for a given speech sound, by examining it at various Signal to Noise Ratios (SNR) presented to NH listeners, and detect the threshold in which listeners recognized the token at least 90% correct (SNR90). For each token, we have determined the time-frequency window corresponding to correct recognition, as well as the conflicting cues. Two sets of tokens T1 and T2 having same consonant-vowels but different talkers with distinct SNR90s had been presented at flat gain (frequency independent) at listeners' most comfortable level (MCL). We studied the effects of frequency fine-tuning of the primary cue by presenting tokens of same consonant but different vowels with similar SNR90s. Additionally, we investigated the role of changing the intensity of primary cue on HI phone recognition, by presenting tokens from both sets T1 and T2. This presentation discusses how the frequency an/or intensity of the primary cue changes the confusion pattern of phone recognition for HI listeners, given a flat gain condition at MCL. We will also explore the effect of these changes on conflicting cues.
The Office of Naval Research Marine Mammal Program, 1990–2006
Authors: Gisiner Robert
Published: April 2018

ONR first stood up a dedicated marine mammal research program in 1990. The initial effort was led by Dan Costa, with the support of experienced ONR program leaders like Mel Briscoe, Bernie Zahuranec, and Steve Zornetzer. The author was privileged to manage the program from 1993 to 2006; a period of rapid expansion of concern about the marine environment accompanied by the desire to put tools for improved understanding in the hands of scientists and decision makers. The emphasis from the start was on multi-disciplinary collaborations. Major research themes included hearing and exploration of Temporary Threshold Shift as a metric of auditory risk; advancement of animal-borne scientific instruments (“tags“); advancement of ocean acoustic monitoring technologies, refinement of field sound exposure experimental methods, and improvement of sound exposure models. Frequent external reviews, including four National Research Council (NRC) reviews, were vital to the quality and credibility of the program. The 2005 NRC review on the Population Consequences of Acoustic Disturbance (PCAD) is a textbook example of how ONR's basic research contributions have had far-reaching consequences that greatly exceeded initial expectations. The convergence of growing concern about manmade sound in the ocean and the ONR model for quality in basic research has had a profound impact on our ability to understand ocean bioacoustics and to make better informed decisions about the potential risks posed by human activities in the marine environment.
Balancing uniform visual appearance with the need for adjustable acoustics in a concert venue: A case study
Authors: Kahn David , Dunham Joshua R. , Aquila Alexander , Cottrell Tyler , Ott Jacob , Roselli Nicholas , Celmer Robert
Published: April 2018

An acoustician’s recommendations for adjustable acoustics curtains in a concert venue sometimes comes into conflict with the architect’s aesthetic vision for the space. The architectural intent is usually for patrons to have a uniform visual experience of the room, regardless of the setting of the adjustable acoustics elements. This leads to the need for architecturally interesting, acoustically transparent elements, such as perforated metal or wooden grills, that can fully or partially hide the adjustable curtains from the eyes of the audience. This paper presents a summary of the collaboration between Acoustic Distinctions and the architectural firm HGA in designing sound-transparent, patterned wood grills that enable a visually attractive and consistent architectural aesthetic, regardless of the settings of the adjustable acoustics curtains behind, in the Kracum Performance Hall at Carleton College. The wood grills—designed collaboratively by the acoustician and architect—were mocked-up and acoustical tests were carried out at the University of Hartford to document their acoustical transparency. Results from those tests will be presented. These results may provide helpful guidelines to future collaborations with architects and acousticians on the design of acoustically transparent surfaces.
Nucleation pressure threshold in acoustic droplet vaporization
Authors: Miles Christopher , Doering Charlie , Kripfgans Oliver D.
Published: April 2018

Acoustic droplet vaporization (ADV) has been studied by several laboratories around the world, including the parametric dependence of its nucleation. In this abstract, we will present our approach of combining classical homogeneous nucleation theory with superharmonic focusing to predict necessary pressures to induce nucleation in ADV. We will show that linear acoustics is a valid approximation to leading order when particle displacements in the sound field are small relative to the radius of the exposed droplet. This is done by perturbation analysis of an axisymmetric compressible inviscid flow about a micrometer-sized droplet with small surface perturbations relative to the mean droplet radius when subjected to an incoming ultrasonic wave. A calibrated single element spherical focus transducer (Olympus A321S 7.5 MHz) was positioned in a water tank above an inverted microscope (Leica DM IL) to emit single ten-cycle bursts. Single droplets (3–30 μm) were placed on ultrasound gel and exposed quasi free-field. Theoretical derivations and predictions will be compared to experimental findings. The ADV nucleation pressure threshold inside the droplet is calculated to be −9.33±0.30 MPa for typical experimental parameters. As a result we are able to predict if a given incident pressure waveform will induce nucleation in an exposed perfluorocarbon droplet.
Enhanced sensitivity of flow detection in small vessels with slow flow by coherent-flow power Doppler
Authors: Dahl Jeremy J.
Published: April 2018

Power Doppler imaging is a commonly used method for the detection of flow. However, the sensitivity of power Doppler in small vessel detection is limited in clinical ultraound scanners by a combination of factors, including the small-diameter of vessels, slow flow through the vessels, the size of the Doppler ensemble, the presence of motion, the presence of noise, and the type of filter used. We have developed an alternative power Doppler imaging technique that enhances flow detection of small vessels and slow flow. This technique utilizes the same principles as power Doppler, but uses the coherence of backscattered blood signal rather than the backscattered signal power. We show that this technique, called coherent flow power Doppler (CFPD), is less sensitive to clutter-based signals and thermal noise and improves signal-to-noise ratio of the flow signal. We show through simulations, phantoms, and in vivo experimentation in human liver that this additional signal-to-noise ratio (7.5-12.5 dB) can be utilized to detect slower flow, improved frame rate (smaller Doppler ensemble), or improve the Doppler image profile. In addition, the technique demonstrates better signal-to-noise ratio for small-sized vessels (less than 2 mm).
Analysis of foldable acoustic arrays from piecewise linear, conformal, and tessellated topologies
Authors: Zou Chengzhe , Harne Ryan L.
Published: April 2018

Arrays of acoustic sources distributed over the tessellated frameworks of origami-inspired folding patterns demonstrate exceptional and straightforward adaptivity of acoustic wave guiding architecture to contrast to the challenges manifest in digital wave guiding control methods. Yet, when the concept of folding arrays is applied to tessellations formed by single patterns, acoustic fields with distinct distributions of energy delivery cannot be realized. To overcome this limitation, here multiple folding patterns are assembled by piecewise geometries that permit the array to conform to unique topologies when reconfigured by physical folding actions. An analytical model is developed to predict the acoustic pressure radiated from the acoustic sources arranged on piecewise-continuous surfaces, while experiments are conducted to demonstrate the concept and validate the model. Parametric investigations are then undertaken to uncover the relations of modularity and folding of the acoustic array and the resulting acoustic energy delivery and distributions. The results find that the assembly of tessellated arrays from multiple distinct folding pattern sub-elements may replicate the acoustic wave guiding of complex acoustic sources that traditionally do not enable adaptive wave radiation properties.
Improving acquisition time of the frequency-specific auditory brainstem response through simultaneous independently random toneburst sequences
Authors: Orlando Mark S. , Maddox Ross K.
Published: April 2018

The frequency-specific auditory brainstem response (ABR) is an objective electroencephalographic (EEG) method for estimating auditory thresholds when behavioral thresholds are not attainable, primarily in infants and toddlers. It is recorded by repeatedly presenting brief, band-limited tonebursts and averaging the scalp potential response. In a typical ABR evaluation, measurements are made at multiple intensities, at multiple frequencies, and in both ears, leading to a large combinatorial space and long test times. Here, we present a method of recording the responses at five frequencies in both ears simultaneously, along with preliminary data demonstrating its effectiveness. We created ten toneburst trains—five octave frequencies (500–8000 Hz) by two ears—for simultaneous presentation. Importantly, the toneburst timing for each train was dictated by an independent random process, rather than being periodic. Independent sequences allow separate computation of the ABR to each of the toneburst trains as the cross-correlation of its timing sequence and the EEG recording. Early results suggest substantial improvements in recording time, particularly at lower stimulus intensities. It also appears that cochlear spread of excitation—a problem at high intensities—is mitigated by our method. This improvement in place specificity is predicted by modeling of auditory nerve activity.
A method for distinguishing tongue surface topology for different categories of speech sound
Authors: Washington Jonathan N. , Washington Paul A.
Published: April 2018

An analytic method has been developed to assist in interpreting data from two-dimensional ultrasound tongue imaging by determining whether the position of the tongue surface significantly differs for two categories of speech sound and, if so, which region is most associated with the difference. Individual tongue traces are modeled as curves in a polar coordinate system around a reference point. Two categories of speech sound are compared as a function of the distance between the traces of the two categories at each arc angle. The regions of the arc with the most significant deviation (i.e., where the categories are best contrasted) are shown by the largest ratio of mean to standard deviation (the greatest number of standard deviations separating the mean tongue surfaces). Categories are most distinguished in regions with more than one standard deviation separating them. A ratio of the angular distance between a point of complete overlap (no contrast) and the maximum positive and negative differentiation points has potential as a speaker-agnostic measure of which regions of tongue position are important at the level of the linguistic variety. To demonstrate this method, its application to the vowel anteriority contrast in several Turkic languages is presented.
Parallel evolution of Batesian mimicry supergene in twoPapiliobutterflies,P. polytesandP. memnon
Authors: Iijima Takuro , Kajitani Rei , Komata Shinya , Lin Chung-Ping , Sota Teiji , Itoh Takehiko , Fujiwara Haruhiko
Published: April 2018

Female-limited polymorphisms underlying Batesian mimicry have evolved independently in two closely related butterfly species.
Freshening by glacial meltwater enhances melting of ice shelves and reduces formation of Antarctic Bottom Water
Authors: Silvano Alessandro , Rintoul Stephen Rich , Peña-Molino Beatriz , Hobbs William Richard , van Wijk Esmee , Aoki Shigeru , Tamura Takeshi , Williams Guy Darvall
Published: April 2018

Glacial meltwater stops bottom-water formation, allowing warm ocean waters to reach Antarctic ice shelves and drive rapid melting.
Low-input and multiplexed microfluidic assay reveals epigenomic variation across cerebellum and prefrontal cortex
Authors: Ma Sai , Hsieh Yuan-Pang , Ma Jian , Lu Chang
Published: April 2018

A microfluidic technology was developed and used to probe epigenomic differences between prefrontal cortex and cerebellum.
Complete and Draft Genome Sequences of Nine Lactobacillus sakei Strains Selected from the Three Known Phylogenetic Lineages and Their Main Clonal Complexes
Authors: Loux Valentin , Coeuret Gwendoline , Zagorec Monique , Champomier Vergès Marie-Christine , Chaillou Stéphane
Published: April 2018

We present here the complete and draft genome sequences of nine
Lactobacillus sakei
strains, selected from the entire range of clonal complexes from the three known lineages of the species. The strains were chosen to provide a wide view of pangenomic and plasmidic diversity for this important foodborne species.
Complete Genome Sequence of the Poly-γ-Glutamate-Synthesizing Bacterium Bacillus subtilis Bs-115
Authors: Wang Fengqing , Gong Lijuan , Zhou Lihong , Liang Jinzhong
Published: April 2018

Bacillus subtilis
Bs-115 was isolated from the soil of a corn field in Yutai County, Jinan City, Shandong Province, People’s Republic of China, and is characterized by the efficient synthesis of poly-γ-glutamate (γ-PGA), with corn saccharification liquid as the sole energy and carbon source during the process of γ-PGA formation. Here, we report the complete genome sequence of
Bacillus subtilis
Bs-115 and the genes associated with poly-γ-glutamate synthesis.
Draft Genome Sequences of 116 Campylobacter jejuni Strains Isolated from Humans, Animals, Food, and the Environment in Brazil
Authors: Frazão Miliane Rodrigues , Cao Guojie , Medeiros Marta Inês Cazentini , Duque Sheila da Silva , Leon Maria Sanchez , Allard Marc William , Falcão Juliana Pfrimer
Published: April 2018

Campylobacter jejuni
is a major zoonotic pathogen that causes foodborne gastroenteritis worldwide. However, clinical cases of campylobacteriosis have been underreported and underdiagnosed in Brazil. Herein, we describe the draft genome sequences of 116
C. jejuni
strains isolated from diverse sources in Brazil.
Draft Genome Sequences of Six Multidrug-Resistant Clinical Strains of Acinetobacter baumannii, Isolated at Two Major Hospitals in Kuwait
Authors: Nasser Kother , Mustafa Abu Salim , Khan Mohd Wasif , Purohit Prashant , Al-Obaid Inaam , Dhar Rita , Al-Fouzan Wadha
Published: April 2018

Acinetobacter baumannii
is an important opportunistic pathogen in global health care settings. Its dissemination and multidrug resistance pose an issue with treatment and outbreak control. Here, we present draft genome assemblies of six multidrug-resistant clinical strains of
A. baumannii
isolated from patients admitted to one of two major hospitals in Kuwait.
Draft Genome Sequences of Pseudomonas sp. Strain 382 and Pantoea coffeiphila 342, Endophytic Bacteria Isolated from Brazilian Guarana [Paullinia cupana (Mart.) Ducke]
Authors: de Siqueira Kátia Aparecida , Liotti Rhavena Graziela , Mendes Tiago Antônio de Oliveira , Soares Marcos Antônio
Published: April 2018

Pseudomonas
sp. strain 382 and
Pantoea coffeiphila
342 are two endophytic bacterial strains isolated from
Paullinia cupana
(guarana) seeds. Their draft genome sizes were 5.96 and 6.38 Mbp, with 315 and 266 scaffolds and 52% and 62% GC content, respectively.
Complete Genome Sequence of Spiroplasma floricola 23-6
T
(ATCC 29989), a Bacterium Isolated from a Tulip Tree (Liriodendron tulipifera L.)
Authors: Tsai Yi-Ming , Wu Pei-Shan , Lo Wen-Sui , Kuo Chih-Horng
Published: April 2018

Spiroplasma floricola
23-6
T
(ATCC 29989) was isolated from the flower surface of a tulip tree (
Liriodendron tulipifera
L.). Here, we report the complete genome sequence of this bacterium to facilitate the investigation of its biology and the comparative genomics among
Spiroplasma
species.
Draft Genome Sequences of Interpatient and Intrapatient Epidemiologically Linked Neisseria gonorrhoeae Isolates
Authors: Hirk Sonja , Lepuschitz Sarah , Cabal Rosel Adriana , Huhulescu Steliana , Blaschitz Marion , Stöger Anna , Stadlbauer Silke , Hasenberger Petra , Indra Alexander , Schmid Daniela , Ruppitsch Werner , Allerberger Franz
Published: April 2018

Neisseria gonorrhoeae
is the causative agent of gonorrhea and was identified by the World Health Organization as an urgent public health threat due to emerging antibiotic resistance. Here, we report 13 draft genome sequences of
N. gonorrhoeae
isolates derived from two epidemiologically linked cases from Austria.
Characterization of Three Novel Linear Neutralizing B-Cell Epitopes in the Capsid Protein of Swine Hepatitis E Virus
Authors: Chen Yiyang , Liu Baoyuan , Sun Yani , Li Huixia , Du Taofeng , Nan Yuchen , Hiscox Julian A. , Zhou En-Min , Zhao Qin
Published: April 2018

Hepatitis E virus (HEV) causes liver disease in humans and is thought to be a zoonotic infection, with domestic animals, including swine and rabbits, being a reservoir. One of the proteins encoded by the virus is the capsid protein. This is likely the major immune-dominant protein and a target for vaccination. Four monoclonal antibodies (MAbs), three novel, 1E4, 2C7, and 2G9, and one previously characterized, 1B5, were evaluated for binding to the capsid protein from genotype 4 swine HEV. The results indicated that
625
DFCP
628
,
458
PSRPF
462
, and
407
EPTV
410
peptides on the capsid protein comprised minimal amino acid sequence motifs recognized by 1E4, 2C7, and 2G9, respectively. The data suggested that 2C7 and 2G9 epitopes were partially exposed on the surface of the capsid protein. Truncated genotype 4 swine HEV capsid protein (sp239, amino acids 368 to 606) can exist in multimeric forms. Preincubation of swine HEV with 2C7, 2G9, or 1B5 before addition to HepG2 cells partially blocked sp239 cell binding and inhibited swine HEV infection. The study indicated that 2C7, 2G9, and 1B5 partially blocked swine HEV infection of rabbits better than 1E4 or normal mouse IgG. The cross-reactivity of antibodies suggested that capsid epitopes recognized by 2C7 and 2G9 are common to HEV strains infecting most host species. Collectively, MAbs 2C7, 2G9, and 1B5 were shown to recognize three novel linear neutralizing B-cell epitopes of genotype 4 HEV capsid protein. These results enhance understanding of HEV capsid protein structure to guide vaccine and antiviral design.

IMPORTANCE
Genotype 3 and 4 HEVs are zoonotic viruses. Here, genotype 4 HEV was studied due to its prevalence in human populations and pig herds in China. To improve HEV disease diagnosis and prevention, a better understanding of the antigenic structure and neutralizing epitopes of HEV capsid protein are needed. In this study, the locations of three novel linear B-cell recognition epitopes within genotype 4 swine HEV capsid protein were characterized. Moreover, the neutralizing abilities of three MAbs specific for this protein, 2C7, 2G9, and 1B5, were studied
in vitro
and
in vivo
. Collectively, these findings reveal structural details of genotype 4 HEV capsid protein and should facilitate development of applications for the design of vaccines and antiviral drugs for broader prevention, detection, and treatment of HEV infection of diverse human and animal hosts.
CD4 T Cell Epitope Specificity and Cytokine Potential Are Preserved as Cells Transition from the Lung Vasculature to Lung Tissue following Influenza Virus Infection
Authors: DiPiazza Anthony , Laniewski Nathan , Rattan Ajitanuj , Topham David J. , Miller Jim , Sant Andrea J.
Published: April 2018

Pulmonary CD4 T cells are critical in respiratory virus control, both by delivering direct effector function and through coordinating responses of other immune cells. Recent studies have shown that following influenza virus infection, virus-specific CD4 T cells are partitioned between pulmonary vasculature and lung tissue. However, very little is known about the peptide specificity or functional differences of CD4 T cells within these two compartments. Using a mouse model of influenza virus infection in conjunction with intravascular labelingin vivo, the cell surface phenotype, epitope specificity, and functional potential of the endogenous polyclonal CD4 T cell response was examined by tracking nine independent CD4 T cell epitope specificities. These studies revealed that tissue-localized CD4 cells were globally distinct from vascular cells in expression of markers associated with transendothelial migration, residency, and micropositioning. Despite these differences, there was little evidence for remodeling of the viral epitope specificity or cytokine potential as cells transition from vasculature to the highly inflamed lung tissue. Our studies also distinguished cells in the pulmonary vasculature from peripheral circulating CD4 T cells, providing support for the concept that the pulmonary vasculature does not simply reflect circulating cells that are trapped within the narrow confines of capillary vessels but rather is enriched in transitional cells primed in the draining lymph node that have specialized potential to enter the lung tissue.

IMPORTANCECD4 T cells convey a multitude of functions in immunity to influenza, including those delivered in the lymph node and others conveyed by CD4 T cells that leave the lymph node, enter the blood, and extravasate into the lung tissue. Here, we show that the transition of recently primed CD4 cells detected in the lung vasculature undergo profound changes in expression of markers associated with tissue localization as they establish residence in the lung. However, this transition does not edit CD4 T cell epitope specificity or the cytokine potential of the CD4 T cells. Thus, CD4 T cells that enter the infected lung can convey diverse functions and have a sufficiently broad viral antigen specificity to detect the complex array of infected cells within the infected tissue, offering the potential for more effective protective function.
Improving local anaesthetic systemic toxicity (LAST) awareness in maternity care using tailored educational tools
Authors: Edwards Amy E , Bowsher Gemma M , Deepak Sahil , Ali Mohamed
Published: April 2018

Local anaesthetic (LA) agents are widely used in maternity care. Although relatively safe, their use does carry risks, the most serious of which is systemic toxicity (LAST). LAST poses a major threat to maternal and neonatal safety due to the frequency of LA administration in maternity care and the under-recognition of toxicity in such settings, which has been reported globally. Our aim was to prevent LAST occurrence in a District General Hospital (DGH) maternity unit by improving staff awareness through the implementation of a tailored educational programme. We used a standardised 14-point questionnaire to evaluate LAST awareness among staff of all disciplines. Domains of interest were LA maximum safe doses, LAST recognition, immediate management and use of antidote. Following baseline assessment, we implemented an educational programme in three stages. Each featured a distinct tool: video presentation, poster and lanyard card. Awareness was reassessed between stages using the same questionnaire. We identified poor baseline awareness across all non-anaesthetic disciplines. Average questionnaire score improved from 3.9/14 (n=23) to 8.1/14 (n=30) during the project period, an increase of 109.3%. Scores improved in all professional groups and a change in workplace culture has been reported. Using a tailored interprofessional educational intervention, we generated an increase in awareness and maintained this over a 4-month period. Improved knowledge and a shift in clinical attitudes towards shared responsibility will reduce avoidable peripartum risk associated with LAST at this DGH. Although the tools used were specific to LAST in this setting, they could be easily adapted for NHS maternity services elsewhere and indeed other areas of care.
Primary ureteral urothelial (transitional cell) carcinoma in a boxer dog
Authors: O Cathasaigh Micheal , Arenas Carolina , Ortiz Ana , Hall Jon L , Rudorf Heike
Published: April 2018

An eight‐year‐old male entire boxer dog was presented by the owner with a four‐week history of haematuria. Abdominal ultrasound identified a moderately dilated left ureter from immediately distal to the renal pelvis to a focal stenosis at the level of L5. Intravenous urography showed a diffusely tortuous proximal left ureter with irregular contrast borders and focal stenosis distally. Left ureteronephrectomy was performed and histology of the left ureter revealed a primary ureteral urothelial (transitional cell) carcinoma infiltrating the ureteral wall. This is the first imaging description of a primary ureteral urothelial carcinoma and only the second description of a primary ureteral urothelial carcinoma in veterinary literature.
Exchange interactions and magnetocaloric effects of the Heusler alloys Ni–Mn–In–R (R = Fe, Co)
Authors: Li Yan-Ru , Su Hui-Ling , Sun Ji-Bing , Li Ying
Published: April 2018

The magnetic interactions and magnetocaloric effects in Ni2Mn[Formula: see text]In[Formula: see text]R[Formula: see text] (x = 0–0.2) (R = Fe, Co) Heusler alloys are investigated by the first-principles and Monte Carlo method. The ab initio calculations provide a basic understanding of the competition of ferromagnetic and antiferromagnetic interactions due to the chemical disorder of the alloy compositions. The thermodynamic properties including magnetization, specific heat and magnetic entropy change are calculated by the finite-temperature Monte Carlo simulations using the exchange couplings and magnetic moments from ab initio calculation as input parameters. The results show that the Fe or Co doping in Ni2Mn[Formula: see text]In[Formula: see text] leads to an increase of magnetic moment and magnetic entropy change but a decrease of magnetic transition temperature with the increase in the Fe or Co contents. This indicates that the transition temperature and magnetocaloric properties of Ni2Mn[Formula: see text]In[Formula: see text] alloy can be tuned by substituting In atom by Fe or Co with different contents.
Hamiltonian mean-field model: effect of temporal perturbation in coupling matrix
Authors: Bhadra Nivedita , Patra Soumen K.
Published: April 2018

The Hamiltonian mean-field (HMF) model is a system of fully coupled rotators which exhibits a second-order phase transition at some critical energy in its canonical ensemble. We investigate the case where the interaction between the rotors is governed by a time-dependent coupling matrix. Our numerical study reveals a shift in the critical point due to the temporal modulation. The shift in the critical point is shown to be independent of the modulation frequency above some threshold value, whereas the impact of the amplitude of modulation is dominant. In the microcanonical ensemble, the system with constant coupling reaches a quasi-stationary state (QSS) at an energy near the critical point. Our result indicates that the QSS subsists in presence of such temporal modulation of the coupling parameter.
The τq-Fourier transform: Covariance and uniqueness
Authors: Kalogeropoulos Nikolaos
Published: April 2018

We propose an alternative definition for a Tsallis entropy composition-inspired Fourier transform, which we call “[Formula: see text]-Fourier transform”. We comment about the underlying “covariance” on the set of algebraic fields that motivates its introduction. We see that the definition of the [Formula: see text]-Fourier transform is automatically invertible in the proper context. Based on recent results in Fourier analysis, it turns that the [Formula: see text]-Fourier transform is essentially unique under the assumption of the exchange of the point-wise product of functions with their convolution.
Optical soliton perturbation in magneto-optic waveguides
Authors: Biswas Anjan , Arnous Ahmed H. , Ekici Mehmet , Sonmezoglu Abdullah , Seadawy Aly R. , Zhou Qin , Mahmood Mohammad F. , Moshokoa Seithuti P. , Belic Milivoj
Published: April 2018

This paper addresses the dynamics of optical solitons in the presence of perturbation terms by the aid of three integration schemes. They are modified simple equation method, trial equation scheme, and the extended trial equation scheme. There are three types of nonlinearities that are studied in this paper which are Kerr law, power law, and logarithmic law. The constraint conditions for the existence of these solitons are also presented.
Femtosecond-pulsed Z-scan study on third- and fifth-order refractive nonlinearities in a side-chain azobenzene copolymer film
Authors: Xue Yuxiong , Wan Yong , Gu Bing
Published: April 2018

By performing the femtosecond-pulsed [Formula: see text]-scan experiments at a wavelength of 780[Formula: see text]nm, we report the observation of simultaneous third- and fifth-order refractive nonlinearities in the film of a side-chain azobenzene copolymer synthesized by free-radical polymerization method. Theoretically, we extend two continuous wave [Formula: see text]-scan theories suitable for the excitation of ultrafast laser pulses. First one is valid only for the situation of the sample with the pure third-order refractive nonlinearity. Second one is applicable when the sample exhibits the simultaneous third- and fifth-order refractive nonlinearities. Both [Formula: see text]-scan theories allow the precise analysis of femtosecond-pulsed [Formula: see text]-scan experimental data. Using the femtosecond time-resolved optical Kerr effect measurements, we estimate the nonlinear response time of the sample to be in the sub-picosecond regime. The physical mechanisms of the observed nonlinearity are also discussed. The high nonlinear figure of merit with ultrafast response in this polymer is desirable in nonlinear photonic devices.
Reproduction of the UV-vis spectra of boron subphthalocyanine chloride in different solvents using time-dependent generalized Kohn–Sham density functionals with first solvation shell
Authors: Chen Xue , Chen Wenlan , Zheng Shaohui
Published: April 2018

Because of the unique physical, chemical and optical characteristics of boron subphthalocyanine chloride, it has been widely applied in different research fields and attracted global researchers. Deep insight into its UV-vis spectrum is required to understand the mechanism of the photon absorption of boron subphthalocyanine chloride in its condensed phase. In the present work, we utilize generalized Kohn–Sham density functionals with a non-equilibrium solvation model to simulate the UV-vis spectra of boron subphthalocyanine chloride in different solvents. Without considering the first solvation shell, we find that the slopes of lines drawn with [Formula: see text]B97XD and CAM-B3LYP results vs. experimental absorption wavelengths are close to 1.0 and root–mean–square deviations are less than 40 nm. We also find that the inclusion of the first solvation shell surrounding boron subphthalocyanine chloride monomers generally makes the calculated results worse. Finally, we discover that the simulated results overestimate oscillator strength of electronic absorption spectra in the ultraviolet region with respect to experimental spectra. These results imply that it may be important to consider the aggregation of solute molecules in order to understand the electronic absorption spectra of subPC in solution
Boosting efficiency of planar heterojunction perovskite solar cells by a low temperature TiCl4 treatment
Authors: Wang Enqi , Chen Peng , Yin Xingtian , Gao Bowen , Que Wenxiu
Published: April 2018

It is well known that electron transport layer (ETL) plays an indispensable role in the planar heterojunction perovskite solar cells (PSCs). TiO2 is widely used as an ETL material due to its excellent transport properties, however, the presence of defects in the TiO2 layer diminishes the power conversion efficiency (PCE) of the devices. Herein, we introduce a method of low-temperature TiCl4 treatment to deposit a TiOx layer on the surface of TiO2 film, which can effectively passivate trap states at the TiO2 surface. Moreover, the treating process is optimized to be 30[Formula: see text]min using a 40[Formula: see text]mM TiCl4 aqueous solution. Benefiting from this, we obtain the champion device with the highest PCE of 18.47%, which is mainly due to the reduction of surface defects and the deposition of the well-crystallized perovskite films. Besides, the modified PSCs exhibit an average PCE of 17.59%, which is much better than the control devices.
Nonuniform Spatial Deformation of Light Fields by Locally Linear Transformations
Authors: Birklbauer Clemens , Schedl David C. , Bimber Oliver
Published: April 2018

Light-field cameras offer new imaging possibilities compared to conventional digital cameras. However, the additional angular domain of light fields prohibits direct application of frequently used image processing algorithms, such as warping, retargeting, or stitching. We present a general and efficient framework for nonuniform light-field warping, which forms the basis for extending many of these image processing techniques to light fields. It propagates arbitrary spatial deformations defined in one light-field perspective consistently to all other perspectives by means of 4D patch matching instead of relying on explicit depth reconstruction. This allows processing light-field recordings of complex scenes with non-Lambertian properties such as transparency and refraction. We show application examples of our framework in panorama light-field imaging, light-field retargeting, and artistic manipulation of light fields.
Programmable 2D Arrangements for Element Texture Design
Authors: Loi Hugo , Hurtut Thomas , Vergne Romain , Thollot Joelle
Published: April 2018

This article introduces a programmable method for designing stationary 2D arrangements for element textures, namely textures made of small geometric elements. These textures are ubiquitous in numerous applications of computer-aided illustration. Previous methods, whether they be example-based or layout-based, lack control and can produce a limited range of possible arrangements. Our approach targets technical artists who will design an arrangement by writing a script. These scripts are using three types of operators:
partitioning operators
for defining the broad-scale organization of the arrangement,
mapping operators
for controlling the local organization of elements, and
merging operators
for mixing different arrangements. These operators are designed so as to guarantee a stationary result, meaning that the produced arrangements will always be repetitive. We show that this simple set of operators is sufficient to reach a much broader variety of arrangements than previous methods. Editing the script leads to predictable changes in the synthesized arrangement, which allows an easy iterative design of complex structures. Finally, our operator set is extensible and can be adapted to application-dependent needs.