bluuebunny/crossref_metadata_2025 huggingface dataset:
Compact high-sensitivity potentiometer for detection of low ion concentrations in liquids
Authors: Balevicius Z. , Lescinskas R. , Celiesiute R. , Stirke A. , Balevicius S. , Kersulis S. , Bleizgys V. , Maciuleviciene R. , Ramanavicius A. , Zurauskiene N.
Published: April 2018

The compact potentiometer, based on an electronic circuit protected from electrostatic and electromagnetic interference, was developed for the measurement of low ion concentrations in liquids. The electronic circuit of the potentiometer, consisting of analogous and digital parts, enables the measurement of fA currents. This makes it possible to perform reliable measurements of ion concentrations in liquids that are as small as 10−8-10−7M. The instrument was tested using electrodes that were selective for tetraphenylphosphonium (TPP+) ions. It was demonstrated that the characteristic response time of the potentiometer electronic circuit to changes in the concentration of these ions in a liquid was in the order of 10 s. An investigation of TPP+ absorption by baker yeast has shown that this device can be successfully used for long term (several hours) measurements with zero signal drift, which was about 1 μV/s. Finally, due to the small dimensions of the electronic circuit (7.5 × 2 × 1.5 cm), this potentiometer can be easily installed at a large apparatus in the laboratory condition (≈25 °C), such as high pulsed electrical generators of magnetic fields that are used in electroporation studies of biological cells.
Design of a seismo-acoustic station for Antarctica
Authors: Contrafatto Danilo , Fasone Rosario , Ferro Angelo , Larocca Graziano , Laudani Giuseppe , Rapisarda Salvatore , Scuderi Luciano , Zuccarello Luciano , Privitera Eugenio , Cannata Andrea
Published: April 2018

In recent years, seismological studies in Antarctica have contributed plenty of new knowledge in many fields of earth science. Moreover, acoustic investigations are now also considered a powerful tool that provides insights for many different objectives, such as analyses of regional climate-related changes and studies of volcanic degassing and explosive activities. However, installation and maintenance of scientific instrumentation in Antarctica can be really challenging. Indeed, the instruments have to face the most extreme climate on the planet. They must be tolerant of very low temperatures and robust enough to survive strong winds. Moreover, one of the most critical tasks is powering a remote system year-round at polar latitudes. In this work, we present a novel seismo-acoustic station designed to work reliably in polar regions. To enable year-round seismo-acoustic data collection in such a remote, extreme environment, a hybrid powering system is used, integrating solar panels, a wind generator, and batteries. A power management system was specifically developed to either charge the battery bank or divert energy surplus to warm the enclosure or release the excess energy to the outside environment. Finally, due to the prohibitive environmental conditions at most Antarctic installation sites, the station was designed to be deployed quickly.
Influence of different gaps among the split targets with gradient potential to the discharge effects generated by hypervelocity impact
Authors: Tang Enling , Zhao Liangliang , Han Yafei , Zhang Qingming , Wang Ruizhi , He Liping , Liu Shuhua
Published: April 2018

Due to the actual situation of spacecraft surface’ charging, such as convex corners, weld line, whalebone and a multiple-interfaces with different materials, all these are main factors leading to uneven charging of spacecraft surface, even creating gradient potential. If the charging spacecraft surface is impacted by debris or micrometeor, discharge effect induced by impacting will pose a serious threat to spacecraft in orbit. So realizing spacecraft charging surface with different potential differences and grasping discharge characteristics are a decisive importance at the different experimental conditions in laboratory. To simulate the spacecraft surface with a gradient potential in laboratory, spacecraft surface is split into different parts, which different gaps reserved in 2 adjacent surface is added resistance to create different potential surfaces, and the high potential surface as a impact target in the split targets. Charging circuit system realizing different gradient potential and discharge test system are built by ourselves, combining with two-stage light gas gun loading system, six sets of experiments have been performed about hypervelocity impact on 2A12 aluminum split targets with gradient potentials. In the experiments, gaps of 2A12 aluminum target are the same among different parts in every experiments, the gaps of the split targets are 2mm, 3mm, 5mm, 7mm and 10mm in the experiments, respectively. And the applied voltage is 300V in all the experiments and high-potential 2A12 aluminum plate as the impact target. The experiments have been performed at the impact velocity of about 3km/s and the incidence angles of 60o and 90o (between projectile flying trajectory and target plane), respectively. Voltage probe and current probes are used for acquiring discharge voltages and currents during the process of the impact. The experimental results showed that the discharge induced by impact plasma were generated among high and low-potential target by forming a plasma discharge channel. With the increasing of the gaps among the high and low-potential targets, the peak values of the discharge current decreased first then increased. When the gaps of split targets reached a certain value, the peak values of the discharge current decreased again. Meanwhile, the gaps among high and low-potential targets was 5mm, the peak value of the discharge current was the smallest. With the increasing of the gaps among the split targets, a primary discharge duration also increased. However, when the gaps among the split targets were greater than 5mm, increasing trend of discharge duration would slow down. When the gaps among the split targets were greater than 7mm, there was a secondary discharge phenomenon, and the physical explanations were given about the influence of different gaps among the split targets on the discharge effects created by hypervelocity impact.
Effects of surface passivation dielectrics on carrier transport in AlGaN/GaN heterostructure field-effect transistors
Authors: Oh Sejoon , Jang Han-Soo , Choi Chel-Jong , Cho Jaehee
Published: April 2018

Dielectric layers prepared by different deposition methods were used for the surface passivation of AlGaN/GaN heterostructure field-effect transistors (HFETs) and the corresponding electrical characteristics were examined. Increases in the sheet charge density and the maximum drain current by approximately 45% and 28%, respectively, were observed after the deposition of a 100 nm-thick SiO2 layer by plasma-enhanced chemical vapor deposition (PECVD) on the top of the AlGaN/GaN HFETs. However, SiO2 deposited by a radio frequency (rf) sputter system had the opposite effect. As the strain applied to AlGaN was influenced by the deposition methods used for the dielectric layers, the carrier transport in the two-dimensional electron gas formed at the interface between AlGaN and GaN was affected accordingly.
Brillouin micro-spectroscopy through aberrations via sensorless adaptive optics
Authors: Edrei Eitan , Scarcelli Giuliano
Published: April 2018

Brillouin spectroscopy is a powerful optical technique for non-contact viscoelastic characterizations which has recently found applications in three-dimensional mapping of biological samples. Brillouin spectroscopy performances are rapidly degraded by optical aberrations and have therefore been limited to homogenous transparent samples. In this work, we developed an adaptive optics (AO) configuration designed for Brillouin scattering spectroscopy to engineer the incident wavefront and correct for aberrations. Our configuration does not require direct wavefront sensing and the injection of a “guide-star”; hence, it can be implemented without the need for sample pre-treatment. We used our AO-Brillouin spectrometer in aberrated phantoms and biological samples and obtained improved precision and resolution of Brillouin spectral analysis; we demonstrated 2.5-fold enhancement in Brillouin signal strength and 1.4-fold improvement in axial resolution because of the correction of optical aberrations.
Sequential Detection of CN- and HSO4- Anions in an Aqueous Environment Utilizing a New Colorimetric Azoimine Receptor: Mimicking Logic Gate Behaviour and a Security Keypad Lock
Authors: Rezaeian Khatereh , Khanmohammadi Hamid , Shabani Nafiseh
Published: April 2018

A new isonicotiamide-based azoimine receptor has been successfully devised and synthesised for dual-recognition of CN− and HSO4− anions in aqueous media (3 : 2 DMSO–water solution). The devised azomethine probe detected lethal cyanide ions under UV-vis spectroscopy through the rapid appearance of an orange colour. More importantly, the colour and spectroscopic changes of the devised chemosensor could be revived upon the addition of HSO4− to the sensor containing cyanide ions. Furthermore, other surveyed anions failed to induce a similar response. Interestingly, based on changes in absorption intensity at a particular wavelength in the presence of two aforementioned anions, as two chemical inputs, an INHIBIT logic gate has been elaborated. Moreover, the reversibility of the sensory system provided an opportunity to present a sequential logic circuit at a molecular level. In accession, the target chemosensor could operate as a molecular keypad lock with sequential chemical inputs of CN− and HSO4− anions.
Performance of a large-scale wetland treatment system in treating tailwater from a sewage treatment plant
Authors: Song Siyuan , Liu Benfa , Zhang Wenjuan , Wang Penghe , Qiao Yajun , Zhao Dehua , Yang Tangwu , An Shuqing , Leng Xin
Published: April 2018

Water quality standards pertaining to effluent from sewage treatment plants (STPs) in China have become more stringent, requiring upgrading of STPs and entailing huge capital expenditure. Wetland treatment systems (WTSs) are a low-cost and highly efficient approach for deep purification of tailwater from STPs. The Hongze WTS (HZ-WTS), a large-scale surface-flow constructed wetland, with a total area of 55.58ha and a treatment capacity of 4×104m3day–1, was built for the disposal of tailwater from STPs. The aim of the present study was to evaluate the performance of HZ-WTP with regard to seasonal variations and to compare treatment costs with those of other STPs. The performance of the HZ-WTS was evaluated in 2013 using online monitoring. HZ-WTS exhibited significant removal efficiency of ammonia nitrogen (NH4+-N), chemical oxygen demand and total phosphorus (mean±s.d., percentage removal efficiency 56.33±70.44, 55.64±18.58 and 88.44±22.71% respectively), whereas there was significant seasonal variation in the efficiency of NH4+-N removal. In addition, the average treatment cost was ¥0.17m–3, significantly lower than the corresponding value for other STPs. Therefore, WTSs are recommended for use with STPs in order to improve waste water quality in a cost-effective manner.
Spatial distribution characteristics and source identification of heavy metals in river waters of the Huaihe River Basin, China
Authors: Yang Jiqiang , Wan Yun , Li Jingjing , Zou Dawei , Leng Xin , An Shuqing
Published: April 2018

Rapid rates of industrialisation and urbanisation have led to heavy metal contamination of many rivers in China. Identification of the main sources of heavy metal contamination in river waters and description of their spatial distribution are essential for the control of river water pollution. In this study, water samples were collected from 218 sampling sites on rivers of the Huaihe River Basin during summer 2014. Fourteen heavy metals were detected (As, Ba, Co, Cr, Fe, Pb, Mn, Mo, Ni, Zn, Se, Sn, Sr and V). The concentrations of these heavy metals showed significant regional variation and the areas could be divided into four groups based on pollution levels: a pollution-free group (Group C), a low pollution group (Group D), a moderate pollution group (Group A), and a high pollution group (Group B). Pearson correlation coefficients verified the common sources of some of the heavy metals. Further analysis revealed that the release of effluents associated with mining, smelting, welding, fertilisers, pesticides and the chemical and electronics industries are the principal sources of heavy metal contamination in the waters of rivers of the Huaihe River Basin.
Self-image and self-reflection
Authors: Chang Nam Fung
Published: April 2018

The futility of decades of government efforts to disseminate Chinese literature has triggered discussions among Chinese scholars on
how to translate and who should be entrusted with this task. Some blame the failure on traditional concepts of translation that
overemphasize faithfulness to the original to the point of disregarding target cultural conditions, but others insist that China
should have control over its cultural export and that Sino-English should be used to internationalize English. Findings show that
traditional concepts should not be blamed, as aggressively source-oriented strategies have been used in outbound translation only
in recent years, and that this shift in translation norms in government-initiated outbound translation has spread to non-literary
text types, and also to Hong Kong and Taiwan. The same kind of aggressiveness has recently been displayed in other forms of
cultural export, triggering resistance in other cultures. All these changes may be attributable to a heightening of cultural
self-image. What is needed to address the issue is cultural self-reflection, which will lead to the awareness that economic growth
does not immediately bring cultural prestige, and that source-initiated cultural export efforts may make little difference in
central cultures. Cultural awareness at a higher level can be achieved only through empathy.
Areal pressure in grammatical evolution
Authors: Cathcart Chundra , Carling Gerd , Larsson Filip , Johansson Niklas , Round Erich
Published: April 2018

This article investigates the evolutionary and spatial dynamics of typological characters in 117 Indo-European languages. We partition types of change (i.e., gain or loss) for each variant according to whether they bring about a simplification in morphosyntactic patterns that must be learned, whether they are neutral (i.e., neither simplifying nor introducing complexity) or whether they introduce a more complex pattern. We find that changes which introduce complexity show significantly less areal signal (according to a metric we devise) than changes which simplify and neutral changes, but we find no significant differences between the latter two groups. This result is compatible with a scenario where certain types of parallel change are more likely to be mediated by advergence and contact between proximate speech communities, while other developments are due purely to drift and are largely independent of intercultural contact.
Eye movements in vocabulary research
Authors: Pellicer-Sánchez Ana , Siyanova-Chanturia Anna
Published: April 2018

The field of vocabulary research is witnessing a growing interest in the use of eye-tracking to investigate topics that have traditionally been examined using offline measures, providing new insights into the processing and learning of vocabulary. During an eye-tracking experiment, participants’ eye movements are recorded while they attend to written or auditory input, resulting in a rich record of online processing behaviour. Because of its many benefits, eye-tracking is becoming a major research technique in vocabulary research. However, before this emerging trend of eye-tracking based vocabulary research continues to proliferate, it is important to step back and reflect on what current studies have shown about the processing and learning of vocabulary, and the ways in which we can use the technique in future research. To this aim, the present paper provides a comprehensive overview of current eye-tracking research findings, both in terms of the processing and learning of single words and formulaic sequences. Current research gaps and potential avenues for future research are also discussed.
Reading a whole book to learn vocabulary
Authors: Nation Paul
Published: April 2018

This paper investigates whether it is a good idea to choose a book that interests you and read it through from the beginning to the end learning all the new words you meet. For the analysis, it is assumed that learners already know the most frequent 3,000 words of English. The criteria used to guide this investigation include the number of unknown words met, the usefulness of the unknown words, the density of the unknown words, and the number of repetitions of the unknown words. Reading a whole book intensively is not a good idea unless the book is a graded reader, a technical text in a relevant subject area, or a set text that would be examined as a part of assessment. Where learners need to do such reading of unsimplified texts, they should be strategic in dealing with unknown vocabulary.
Loanword proportion in vocabulary size tests
Authors: Laufer Batia , Levitzky-Aviad Tami
Published: April 2018

We investigated the effect of English-Hebrew loanwords on English vocabulary test scores when the number of loanwords in the test is random and when it is representative of their proportion in the vocabulary lists from which the test items were taken. 303 EFL learners, speakers of Hebrew as L1, at three L2 proficiency levels, received tests with no loanwords, with a representative number of loanwords and with a random number of loanwords in four modalities: word form recall, word meaning recall, word form recognition, word meaning recognition. Though different effects were found for different modalities and different language proficiencies, the score increases from the representative loanword test version to the random loanword version were low and the effect sizes of the differences were very low. We suggest that the inclusion of loanwords in vocabulary tests may not inflate the true vocabulary knowledge score.
The effect of out-of-class exposure to English language media on learners’ vocabulary knowledge
Authors: Peters Elke
Published: April 2018

The aim of this study is to investigate (1) how often Flemish English-as-a-foreign language learners are exposed to English language media outside of the classroom, (2) whether current out-of-class exposure to English language media is related to learners’ vocabulary knowledge, and (3) whether length of instruction (three or six years), gender, and out-of-class exposure to English language media affect Flemish learners’ vocabulary. Data were collected with 79 English-as-a-foreign language learners. They were administered a frequency-based vocabulary test and a questionnaire. The findings of this study show that Flemish English-as-a-foreign language learners are frequently exposed to English language media. The results also indicate a positive relationship between learners’ vocabulary knowledge and exposure to non-subtitled TV programs and movies, the Internet, and written print (books, magazines). Finally, both length of instruction and current out-of-class exposure to English language media had an effect on learners’ vocabulary knowledge, but out-of-class exposure had a larger effect than length of instruction.
Examining incidental vocabulary acquisition from captioned video
Authors: Jelani Nurul Aini Mohd , Boers Frank
Published: April 2018

Previous comparisons of vocabulary uptake from captioned and uncaptioned audio-visual materials have almost consistently furnished evidence in favour of captioned materials. However, it is possible that many such comparative studies gave an advantage to the captioned input conditions by virtue of their use of written word prompts in the tests. The present study therefore examines whether aurally presented test prompts yield equally compelling evidence for the superiority of captioned over uncaptioned video. Intermediate EFL learners watched a ten-minute TED Talks video either with or without captions and were subsequently given a word recognition and a word meaning test, with half of the test prompts presented in print and the other half presented aurally. While the results of the word recognition test were inconclusive, the word meaning test yielded significantly better scores by the group that watched the captioned video. However, this was due entirely to their superior scores on the printed word prompts, not the aural ones. This suggests that evaluations of the benefits of captions for vocabulary acquisitions should take input-modality – test-modality congruency into account.
Evaluative morphology in the verbal domain
Authors: Németh Boglárka , Sőrés Anna
Published: April 2018

So far, evaluative morphology has received less attention in the verbal domain than in the nominal and adjectival ones. This paper shows that – besides frequentative morphemes like-gAtand preverbs liketele-‘full’, le- ‘down’, fel ‘up’, etc. – in Hungarian events can be evaluated by means of the verbalizer suffix-kVdik. This formation is unusual in evaluative morphology since it is a category-changing operation. The suffix-kVdikcan be attached to adjectives and to nouns expressing a profession or an occupation. Depending on the speaker’s intention, the morphologically complex verb suffixed with-kVdikcan attribute to the activity an evaluative, mostly pejorative meaning. The paper suggests that this phenomenon goes beyond evaluative morphology and can be better analyzed in terms of morphopragmatics.
What to Eat When Having a Millennial over for Dinner
Authors: Conley Kelsey L , Lusk Jayson L
Published: April 2018

Millenials are the generation everyone is talking about and the generation who loves to talk about themselves. More than just a media buzzword, researchers, marketers, and retailers are interested in how the soon‐to‐be‐largest segment of the population is making food purchasing decisions. This paper uses the difference‐in‐difference method to determine the causal “millennial effect” on the share of income spent on various food expenditure categories. Data from the Bureau of Labor Statistics’ Consumer Expenditure Survey was used to identify how young people’s food expenditures compare to older people’s in 2015 and in 1980. Results indicate significant “millennial effects” that might have policy implications for future health care spending. Millennials have higher demand for cereal, beef, pork, poultry, eggs, and fresh fruit and lower demand for “other” food, and for food away from home relative to what would have been expected from the eating patterns of the young and old 35 years prior.
Aortic Pulse Pressure Does Not Adequately Index Cardiovascular Risk Factor-Related Changes in Aortic Stiffness and Forward Wave Pressure
Authors: Motau Tshegofatso H , Norton Gavin R , Sareli Pinhas , Woodiwiss Angela J
Published: April 2018

BACKGROUND

Through the impact of conventional risk factors on arteries, several changes in aortic function contribute to cardiovascular events. It is nevertheless uncertain whether these effects are accurately reflected by changes in central aortic pulse pressure (PPc). We, therefore, aimed to determine the extent to which relations between modifiable risk factors and aortic function translate into increases in PPc.

METHODS

In 1,232 black South Africans from the South West Township (SOWETO) of Johannesburg, we determined risk factors and aortic function from carotid-femoral pulse wave velocity (PWV), aortic PPc, forward wave pressures (Pf), and reflected (backward) wave pressures (Pb) (applanation tonometry and SphygmoCor software).

RESULTS

With adjustments for alternative risk factors and distending pressure (mean arterial pressure (MAP)), diabetes mellitus (treatment or HbA1c > 6.5%, n = 151) was associated with an increased PWV (7.10 ± 2.09 vs. 6.17 ± 2.00 m/s, P < 0.0001), and Pf (26 ± 8 vs. 24 ± 8 mm Hg, P < 0.005), but neither brachial PP (46 ± 14 vs. 45 ± 13, P = 0.19), PPc (36 ± 12 vs. 35 ± 11 mm Hg, P = 0.48), nor Pb (17 ± 6 vs. 17 ± 6 mm Hg, P = 0.83). Moreover, independent of alternative risk factors and MAP, uncontrolled hypertension (office blood pressure > 140/90 mm Hg, n = 433) was associated with an increased Pf (26 ± 12 vs. 24 ± 10 mm Hg, P < 0.01), but not with changes in brachial PP (45 ± 19 vs. 44 ± 17, P = 0.75), PPc (35 ± 16 vs. 35 ± 15 mm Hg, P = 0.93), or Pb (18 ± 8 vs. 17 ± 8 mm Hg, P = 0.46).

CONCLUSIONS

Neither brachial nor aortic PP are adequate indexes of relations between the modifiable conventional risk factors, uncontrolled hypertension or diabetes mellitus, and risk-related aortic functional changes.
Accurate prediction of orthologs in the presence of divergence after duplication
Authors: Lafond Manuel , Meghdari Miardan Mona , Sankoff David
Published: April 2018

Motivation

When gene duplication occurs, one of the copies may become free of selective pressure and evolve at an accelerated pace. This has important consequences on the prediction of orthology relationships, since two orthologous genes separated by divergence after duplication may differ in both sequence and function. In this work, we make the distinction between the primary orthologs, which have not been affected by accelerated mutation rates on their evolutionary path, and the secondary orthologs, which have. Similarity-based prediction methods will tend to miss secondary orthologs, whereas phylogeny-based methods cannot separate primary and secondary orthologs. However, both types of orthology have applications in important areas such as gene function prediction and phylogenetic reconstruction, motivating the need for methods that can distinguish the two types.

Results

We formalize the notion of divergence after duplication and provide a theoretical basis for the inference of primary and secondary orthologs. We then put these ideas to practice with the Hybrid Prediction of Paralogs and Orthologs (HyPPO) framework, which combines ideas from both similarity and phylogeny approaches. We apply our method to simulated and empirical datasets and show that we achieve superior accuracy in predicting primary orthologs, secondary orthologs and paralogs.

Availability and implementation

HyPPO is a modular framework with a core developed in Python and is provided with a variety of C++ modules. The source code is available at https://github.com/manuellafond/HyPPO.

Supplementary information

Supplementary data are available at Bioinformatics online.
A unifying framework for joint trait analysis under a non-infinitesimal model
Authors: Johnson Ruth , Shi Huwenbo , Pasaniuc Bogdan , Sankararaman Sriram
Published: April 2018

Motivation

A large proportion of risk regions identified by genome-wide association studies (GWAS) are shared across multiple diseases and traits. Understanding whether this clustering is due to sharing of causal variants or chance colocalization can provide insights into shared etiology of complex traits and diseases.

Results

In this work, we propose a flexible, unifying framework to quantify the overlap between a pair of traits called UNITY (Unifying Non-Infinitesimal Trait analYsis). We formulate a Bayesian generative model that relates the overlap between pairs of traits to GWAS summary statistic data under a non-infinitesimal genetic architecture underlying each trait. We propose a Metropolis–Hastings sampler to compute the posterior density of the genetic overlap parameters in this model. We validate our method through comprehensive simulations and analyze summary statistics from height and body mass index GWAS to show that it produces estimates consistent with the known genetic makeup of both traits.

Availability and implementation

The UNITY software is made freely available to the research community at: https://github.com/bogdanlab/UNITY.

Supplementary information

Supplementary data are available at Bioinformatics online.
Quantifying the similarity of topological domains across normal and cancer human cell types
Authors: Sauerwald Natalie , Kingsford Carl
Published: April 2018

Motivation

Three-dimensional chromosome structure has been increasingly shown to influence various levels of cellular and genomic functions. Through Hi-C data, which maps contact frequency on chromosomes, it has been found that structural elements termed topologically associating domains (TADs) are involved in many regulatory mechanisms. However, we have little understanding of the level of similarity or variability of chromosome structure across cell types and disease states. In this study, we present a method to quantify resemblance and identify structurally similar regions between any two sets of TADs.

Results

We present an analysis of 23 human Hi-C samples representing various tissue types in normal and cancer cell lines. We quantify global and chromosome-level structural similarity, and compare the relative similarity between cancer and non-cancer cells. We find that cancer cells show higher structural variability around commonly mutated pan-cancer genes than normal cells at these same locations.

Availability and implementation

Software for the methods and analysis can be found at https://github.com/Kingsford-Group/localtadsim
Strand-seq enables reliable separation of long reads by chromosome via expectation maximization
Authors: Ghareghani Maryam , Porubskỳ David , Sanders Ashley D , Meiers Sascha , Eichler Evan E , Korbel Jan O , Marschall Tobias
Published: April 2018

Motivation

Current sequencing technologies are able to produce reads orders of magnitude longer than ever possible before. Such long reads have sparked a new interest in de novo genome assembly, which removes reference biases inherent to re-sequencing approaches and allows for a direct characterization of complex genomic variants. However, even with latest algorithmic advances, assembling a mammalian genome from long error-prone reads incurs a significant computational burden and does not preclude occasional misassemblies. Both problems could potentially be mitigated if assembly could commence for each chromosome separately.

Results

To address this, we show how single-cell template strand sequencing (Strand-seq) data can be leveraged for this purpose. We introduce a novel latent variable model and a corresponding Expectation Maximization algorithm, termed SaaRclust, and demonstrates its ability to reliably cluster long reads by chromosome. For each long read, this approach produces a posterior probability distribution over all chromosomes of origin and read directionalities. In this way, it allows to assess the amount of uncertainty inherent to sparse Strand-seq data on the level of individual reads. Among the reads that our algorithm confidently assigns to a chromosome, we observed more than 99% correct assignments on a subset of Pacific Bioscience reads with 30.1× coverage. To our knowledge, SaaRclust is the first approach for the in silico separation of long reads by chromosome prior to assembly.

Availability and implementation

https://github.com/daewoooo/SaaRclust
On the Topological Rigidity of Compact Self-shrinkers in ℝ3
Authors: Mramor Alexander , Wang Shengwen
Published: April 2018

In this note we show that self-shrinkers in $\mathbb R^{3}$ are “topologically standard” in that any genus g compact self-shrinker is ambiently isotopic to the standard genus g embedded surface in $\mathbb R^{3}$. As a consequence self-shrinking tori are unknotted.
Long-Term Outcome of Spinal Cord Stimulation in Failed Back Surgery Syndrome: 20 Years of Experience With 224 Consecutive Patients
Authors: Nissen Mette , Ikäheimo Tiina-Mari , Huttunen Jukka , Leinonen Ville , von und zu Fraunberg Mikael
Published: April 2018

BACKGROUND

Failed back surgery syndrome (FBSS) is a challenging condition that lacks a curative treatment. In selected patients, spinal cord stimulation (SCS) has provided a satisfactory outcome.

OBJECTIVE

To evaluate the long-term outcome of SCS in FBSS, as measured by (1) the explantation rate, (2) complications, and (3) patient satisfaction with the global perceived effect (GPE).

METHODS

We studied 224 consecutive FBSS patients who underwent an SCS trial with surgically implanted leads at our hospital between January 1996 and December 2014. The patients’ satisfaction with the GPE of treatment was measured through a postal questionnaire at the end of follow-up.

RESULTS

Based on a 1-wk trial, permanent SCS was implanted in 175 (78%) patients. Out of these patients, 153 (87%) reported satisfactory outcomes after 2 mo. During the mean follow-up of 6 yr, 34 (19%) of SCS devices were permanently explanted due to inadequate pain relief, and 11 (6%) were explanted for other reasons.

Electrode revision due to inadequate pain relief was done for 22 patients. In total, 26 complications were reported due to: 7 deep infections, 11 hardware malfunctions, 1 subcutaneous hematoma, 4 instances of discomfort due to the pulse generator, and 3 electrode migrations.

One hundred thirty patients (74%) continued with SCS until the end of follow-up. Of them, 61 (47%) returned the questionnaire, and 42 (69%) reported substantially improved or better GPE.

CONCLUSION

SCS can provide a good outcome in the treatment of FBSS. Patient selection could be further improved by developing novel predictive biomarkers.
Models for Analyzing Zero-Inflated and Overdispersed Count Data: An Application to Cigarette and Marijuana Use
Authors: Pittman Brian , Buta Eugenia , Krishnan-Sarin Suchitra , O’Malley Stephanie S , Liss Thomas , Gueorguieva Ralitza
Published: April 2018

Introduction

This article describes different methods for analyzing counts and illustrates their use on cigarette and marijuana smoking data.

Methods

The Poisson, zero-inflated Poisson (ZIP), hurdle Poisson (HUP), negative binomial (NB), zero-inflated negative binomial (ZINB), and hurdle negative binomial (HUNB) regression models are considered. The different approaches are evaluated in terms of the ability to take into account zero-inflation (extra zeroes) and overdispersion (variance larger than expected) in count outcomes, with emphasis placed on model fit, interpretation, and choosing an appropriate model given the nature of the data. The illustrative data example focuses on cigarette and marijuana smoking reports from a study on smoking habits among youth e-cigarette users with gender, age, and e-cigarette use included as predictors.

Results

Of the 69 subjects available for analysis, 36% and 64% reported smoking no cigarettes and no marijuana, respectively, suggesting both outcomes might be zero-inflated. Both outcomes were also overdispersed with large positive skew. The ZINB and HUNB models fit the cigarette counts best. According to goodness-of-fit statistics, the NB, HUNB, and ZINB models fit the marijuana data well, but the ZINB provided better interpretation.

Conclusion

In the absence of zero-inflation, the NB model fits smoking data well, which is typically overdispersed. In the presence of zero-inflation, the ZINB or HUNB model is recommended to account for additional heterogeneity. In addition to model fit and interpretability, choosing between a zero-inflated or hurdle model should ultimately depend on the assumptions regarding the zeros, study design, and the research question being asked.

Implications

Count outcomes are frequent in tobacco research and often have many zeros and exhibit large variance and skew. Analyzing such data based on methods requiring a normally distributed outcome are inappropriate and will likely produce spurious results. This study compares and contrasts appropriate methods for analyzing count data, specifically those with an over-abundance of zeros, and illustrates their use on cigarette and marijuana smoking data. Recommendations are provided.
Giant Olfactory Groove Meningioma—2-Staged Approach: 2-Dimensional Operative Video
Authors: Todeschini Alexandre B , Shahein Mostafa , Montaser Alaa S , Hardesty Douglas , Otto Bradley A , Carrau Ricardo L , Prevedello Daniel M
Published: April 2018

A 42-yr-old female presented with an olfactory groove meningioma causing progressive vision loss and anosmia. Given the size of the tumor, we opted for a 2-stage surgery: endoscopic endonasal approach (EEA) followed by a craniotomy. Stage I surgery was a transcribriform transplanum EEA using a binostril 4-hand/2 surgeons (ENT and neuro) technique, with the patient positioned supine with the head slightly turned to the right side and tilted to the left, fixed in a 3-pin head clamp, under imaging guidance, in which we drilled out all the affected skull base bone, devascularized and debulked the tumor. Stage II surgery was done through a right frontotemporal craniotomy 2 mo later. The surgery and postoperative period was uneventful with no complications and no need for further reconstruction of the skull base. The patient's vision was normalized. Postoperative magnetic resonance imaging (MRI) confirmed a Simpson Grade 1 resection.

 The rationale behind this staged approach is that we have found when using a transcranial 1-stage approach the brain edema and necessary retraction required for resection leads to brain injury, oftentimes readily identified in the diffusion-weighted imaging MRI which are associated with different degrees of cognitive impairment. The skull base bone involved is usually not removed via transcranial approaches.

 Despite requiring a second surgery, this staged approach allows a true total resection (including the affected bone) and in the transcranial stage the brain is more relaxed, with less edema, reducing the need for retraction, which may lead to a better outcome.

 The patient has given assent and written consent for videos, images, or clinical or genetic information to be published.
Pathogenic Streptomyces spp. Abundance Affected by Potato Cultivars
Authors: Nahar Kamrun , Goyer Claudia , Zebarth Bernie J. , Burton David L. , Whitney Sean
Published: April 2018

Potato cultivars vary in their tolerance to common scab; however, how they affect common scab-causing Streptomyces spp. populations over time is poorly understood. This study investigated the effects of potato cultivar on pathogenic Streptomyces spp. abundance, measured using quantitative PCR, in three spatial locations in a common scab-infested field: (i) soil close to the plant (SCP); (ii) rhizosphere soil (RS); and (iii) geocaulosphere soil (GS). Two tolerant (Gold Rush, Hindenburg) and two susceptible cultivars (Green Mountain, Agria) were tested. The abundance of pathogenic Streptomyces spp. significantly increased in late August compared with other dates in RS of susceptible cultivars in both years. Abundance of pathogenic Streptomyces spp., when averaged over locations and time, was significantly greater in susceptible cultivars compared with tolerant cultivars in 2014. Principal coordinates analysis showed that SCP and RS soil properties (pH, organic carbon, and nitrogen concentrations) explained 68 and 76% of total variation in Streptomyces spp. abundance among cultivars in 2013, respectively, suggesting that cultivars influenced common scab pathogen growth conditions. The results suggested that the genetic background of potato cultivars influenced the abundance of pathogenic Streptomyces spp., with five to six times more abundant Streptomyces spp. in RS of susceptible cultivars compared with tolerant cultivars, which would result in substantially more inoculum left in the field after harvest.
Gravitational-wave astronomy: delivering on the promises
Authors: Schutz B. F.
Published: April 2018

Now that LIGO and Virgo have begun to detect gravitational-wave events with regularity, the field of gravitational-wave astronomy is beginning to realize its promise. Binary black holes and, very recently, binary neutron stars have been observed, and we are already learning much from them. The future, with improved sensitivity, more detectors and detectors like LISA in different frequency bands, has even more promise to open a completely hidden side of the Universe to our exploration.

This article is part of a discussion meeting issue ‘The promises of gravitational-wave astronomy’.
Quasi-monolithic mirror suspensions in ground-based gravitational-wave detectors: an overview and look to the future
Authors: van Veggel Anna-Maria A.
Published: April 2018

At the commencement of a new era in astrophysics, with added information from direct detections of gravitational-wave (GW) signals, this paper is a testament to the quasi-monolithic suspensions of the test masses of the GW detectors that have enabled the opening of a new window on the universe. The quasi-monolithic suspensions are the final stages in the seismic isolation of the test masses in GW detectors, and are specifically designed to introduce as little thermal noise as possible. The history of the development of the fused-silica quasi-monolithic suspensions, which have been so essential for the first detections of GWs, is outlined and a glimpse into the status of research towards quasi-monolithic suspensions made of sapphire and silicon is given.

This article is part of a discussion meeting issue ‘The promises of gravitational-wave astronomy’.
Characterizing transient noise in the LIGO detectors
Authors: Nuttall L. K.
Published: April 2018

Data from the LIGO detectors typically contain many non-Gaussian noise transients which arise due to instrumental and environmental conditions. These non-Gaussian transients can be an issue for the modelled and unmodelled transient gravitational-wave searches, as they can mask or mimic a true signal. Data quality can change quite rapidly, making it imperative to track and find new sources of transient noise so that data are minimally contaminated. Several examples of transient noise and the tools used to track them are presented. These instances serve to highlight the diverse range of noise sources present at the LIGO detectors during their second observing run.

This article is part of a discussion meeting issue ‘The promises of gravitational-wave astronomy’.
Gravitational wave detection using laser interferometry beyond the standard quantum limit
Authors: Heurs M.
Published: April 2018

Interferometric gravitational wave detectors (such as advanced LIGO) employ high-power solid-state lasers to maximize their detection sensitivity and hence their reach into the universe. These sophisticated light sources are ultra-stabilized with regard to output power, emission frequency and beam geometry; this is crucial to obtain low detector noise. However, even when all laser noise is reduced as far as technically possible, unavoidable
quantum noise
of the laser still remains. This is a consequence of the Heisenberg Uncertainty Principle, the basis of quantum mechanics: in this case, it is fundamentally impossible to simultaneously reduce both the phase noise and the amplitude noise of a laser to arbitrarily low levels. This fact manifests in the detector noise budget as two distinct noise sources—photon shot noise and quantum radiation pressure noise—which together form a lower boundary for current-day gravitational wave detector sensitivities, the standard quantum limit of interferometry. To overcome this limit, various techniques are being proposed, among them different uses of non-classical light and alternative interferometer topologies. This article explains how quantum noise enters and manifests in an interferometric gravitational wave detector, and gives an overview of some of the schemes proposed to overcome this seemingly fundamental limitation, all aimed at the goal of higher gravitational wave event detection rates.

This article is part of a discussion meeting issue ‘The promises of gravitational-wave astronomy’.
Control of cell behaviour through nanovibrational stimulation: nanokicking
Authors: Robertson Shaun N. , Campsie Paul , Childs Peter G. , Madsen Fiona , Donnelly Hannah , Henriquez Fiona L. , Mackay William G. , Salmerón-Sánchez Manuel , Tsimbouri Monica P. , Williams Craig , Dalby Matthew J. , Reid Stuart
Published: April 2018

Mechanical signals are ubiquitous in our everyday life and the process of converting these mechanical signals into a biological signalling response is known as mechanotransduction. Our understanding of mechanotransduction, and its contribution to vital cellular responses, is a rapidly expanding field of research involving complex processes that are still not clearly understood. The use of mechanical vibration as a stimulus of mechanotransduction, including variation of frequency and amplitude, allows an alternative method to control specific cell behaviour without chemical stimulation (e.g. growth factors). Chemical-independent control of cell behaviour could be highly advantageous for fields including drug discovery and clinical tissue engineering. In this review, a novel technique is described based on nanoscale sinusoidal vibration. Using finite-element analysis in conjunction with laser interferometry, techniques that are used within the field of gravitational wave detection, optimization of apparatus design and calibration of vibration application have been performed. We further discuss the application of nanovibrational stimulation, or ‘nanokicking’, to eukaryotic and prokaryotic cells including the differentiation of mesenchymal stem cells towards an osteoblast cell lineage. Mechanotransductive mechanisms are discussed including mediation through the Rho-A kinase signalling pathway. Optimization of this technique was first performed in two-dimensional culture using a simple vibration platform with an optimal frequency and amplitude of 1 kHz and 22 nm. A novel bioreactor was developed to scale up cell production, with recent research demonstrating that mesenchymal stem cell differentiation can be efficiently triggered in soft gel constructs. This important step provides first evidence that clinically relevant (three-dimensional) volumes of osteoblasts can be produced for the purpose of bone grafting, without complex scaffolds and/or chemical induction. Initial findings have shown that nanovibrational stimulation can also reduce biofilm formation in a number of clinically relevant bacteria. This demonstrates additional utility of the bioreactor to investigate mechanotransduction in other fields of research.

This article is part of a discussion meeting issue ‘The promises of gravitational-wave astronomy’.
Electrophysiological characterization and MCH/orexin neuronal distribution in the lateral hypothalamus of naked mole-rats (Heterocephalus glaber)
Authors: Husson Zoé , Apergis-Schoute John , Smith Ewan St John
Published: April 2018

The lateral hypothalamus (LH) controls various homeostatic processes, including sleep-wake cycles, energy balance and thermoregulation in many mammalian species. In the LH, melanin-concentrating hormone (MCH) and hypocretin/orexin (HO) containing neurons differentially regulate these processes. Naked mole-rats (NMR) (Heterocephalus glaber) are eusocial mammals with remarkable physiological peculiarities including extreme longevity without significant weight gain and absence of thermoregulation. Altered hypothalamic function could potentially underlie the unusual NMR phenotypes, but to date electrophysiological characterization of LH NMR neurons and expression of MCH and HO is missing. Here, we performed whole-cell recordings from LH neurons in acute NMR and mouse brain slices and found that NMR and mouse neuronal basic properties and activities were comparable. Additionally, we showed that both MCH-positive and HO-positive neuronal populations exist in the NMR hypothalamus and although the majority of MCH- and HO-positive neurons are located in the LH, as previously described in rodents, significant differences exist in MCH/HO distribution in other NMR hypothalamic areas. These results indicate that NMR LH neurons are comparable to mouse neurons with respect to their electrophysiological properties, but differences in the neuronal MCH and HO populations in hypothalamic regions exist and may contribute to the adaptive changes seen in NMR homeostatic processes.