bluuebunny/crossref_metadata_2025 huggingface dataset:
Binding of trivalent ions on fatty acid Langmuir monolayer: Fe3+ versus La3+
Authors: Sung Woongmo , Krem Sona , Kim Doseok
Published: July 2018

Langmuir monolayers consisting of fatty acid molecules were prepared on solutions of FeCl3 and LaCl3 to investigate adsorption of trivalent metal ions on carboxylic headgroups by using sum-frequency vibrational spectroscopy. Fe3+ ions bound to the fatty acid headgroups only in the form of hydroxide complexes (Fe(OH)x+3−x), and sum-frequency intensity of water stretch modes increased markedly upon adsorption of ion hydroxide. On the other hand, La3+ ions bound to the charged anionic headgroup as bare trivalent ions. Upon Fe(OH)x+3−x adsorption, the sum-frequency spectrum of carboxyl headgroups showed significant redshift which is opposite to the case of La3+ as well as those for alkali (Na+, K+) and alkali earth metal (Ca2+, Mg2+) ions, which also supports that Fe3+ binding is by covalent metal-ligand bonding, while La3+ binding is by Coulomb attraction.
Resonant-type piezoelectric inertial linear motor based on the optimization of a dual stage tuning fork transducer
Authors: Pan Qiaosheng , Wang Kailun , Miao Enming , Wu Ye , Shu Shuangbao , Xu Xin , Lei Xiujun
Published: July 2018

A dual stage tuning fork transducer (DSTFT) is designed as a stator for a resonant-type inertial linear motor. The first- and second-layer resonant frequencies of DSTFT are automatically adjusted with a ratio of 1:2 by using an ANSYS optimization design algorithm, and a resonant-type sawtooth-shaped mechanical waveform is generated by composing the two resonant vibrations of DSTFT. An inertial linear motor prototype is fabricated and tested. Experimental results confirmed the effectiveness of the designed transducer. The no-load maximum speed is 21.5 mm/s with a driving voltage of 67.2 Vp-p at a base frequency of 2831 Hz. The linear speed is 10.5 mm/s, and the drag load is 0.02 N at a preload force of 1 N and a driving voltage of 114 Vp-p for the base frequency. The movement direction could be reversed by changing the driving voltage phase.
Comparison of measured pinch parameters versus pressure for SABALAN1 plasma focus facility against computed values using Lee model code
Authors: Karimi F. S. , Saviz S. , Ghoranneviss M. , Salem M. K. , Aghamir F. M.
Published: July 2018

In this paper, we have studied the effect of working gas pressure on plasma pinch properties in a Mather type plasma focus (2 kJ, 20 kV, 10 μF), named SABALAN1. Argon at the various operating pressures ranging from 0.1-1.2 Torr has been used as working gas. The total current waveform has been measured for different pressures. Also, a numerical simulation was done using Lee model code to perform numerical experiments in SABALAN1. The numerical simulation was used to compute argon soft x-ray yield as a function of pressure, to anticipate the maximum soft x-ray efficiency at optimum operating gas pressure. The Lee model was configured for SABALAN1, by fitting a simulated discharge current waveform against a measured discharge current waveform was obtained by numerically integrating the output of a dI/dt calibrated Rogowski coil. The experimental and simulation curves for plasma pinch properties have been plotted. Some of the dynamic parameters of the plasma and the characteristics of the plasma pinch have been displayed at different argon pressures in two tables. In addition, the chart of the normalized parameters of the plasma pinch has been plotted in terms of pressure. The results of experimentally measured and numerical simulation show that better pinches with attention to their plasma pinch characteristics, generally were dependent on pressure and the best pinch is obtained at 0.6-0.7 Torr for argon at 14 kV in SABALAN1. Furthermore, in high pressures (higher than 0.7 Torr in our experiments), the discharge current can behave as short circuit discharge and resembles that of a simple L-C-R discharge which is a damped sinusoidal. Comparison of the experimental and numerical curves shows sensible agreement in some plasma pinch properties such as the time to pinch and depth of focus. The results from charts and tables have been discussed.
Unabsorbed light beamlets for diagnosing cross-beam energy transfer
Authors: Edgell D. H. , Katz J. , Turnbull D. P. , Froula D. H.
Published: July 2018

A new diagnostic has been fielded on OMEGA to diagnose cross-beam energy transfer (CBET) during direct-drive implosions. Unabsorbed light from each OMEGA laser beam is imaged as a distinct “spot” onto a gated optical imager. Each spot is in essence the endpoint of a beamlet of light that originates from different regions of each beam profile and follows a path determined by refraction. The intensity of light in the beamlet varies along its path as a result of absorption and CBET with other beamlets. This diagnostic allows the investigation of the effects of CBET on laser energy from specific locations of the beam profile. The diagnostic records images in two 200-ps time windows and includes a Wollaston prism to split each beamlet into two orthogonal polarizations recorded on separate images, allowing the absolute polarization of each beamlet to be determined. This diagnostic has provided the first evidence of polarization rotation caused by CBET during direct-drive implosions.
Quasi-perpendicular fast magnetosonic shock with wave precursor in collisionless plasma
Authors: Moreno Q. , Dieckmann M. E. , Ribeyre X. , d'Humières E.
Published: July 2018

A one-dimensional particle-in-cell simulation tracks a fast magnetosonic shock over time scales comparable with an inverse ion gyrofrequency. The magnetic pressure is comparable to the thermal pressure upstream. The shock propagates across a uniform background magnetic field with a pressure that equals the thermal pressure upstream at the angle 85° at a speed that is 1.5 times the fast magnetosonic speed in the electromagnetic limit. Electrostatic contributions to the wave dispersion increase its phase speed at large wave numbers, which leads to a convex dispersion curve. A fast magnetosonic precursor forms ahead of the shock with a phase speed that exceeds the fast magnetosonic speed by about ∼30%. The wave is slower than the shock, and hence, it is damped.
Laser-induced fluorescence detection of the elusive SiCF free radical
Authors: Rothschopf Gretchen , Smith Tony C. , Clouthier Dennis J.
Published: July 2018

The SiCF free radical has been spectroscopically identified for the first time. The radical was produced in an electric discharge jet using CF3Si(CH3)3 or CF3SiH3 vapor in high pressure argon as the precursor. The laser-induced fluorescence spectrum of the Ã∑+2−X̃∏2 band system in the 610 − 550 nm region was recorded and the ∏3/22 spin component of the 0—0 band was studied at high resolution. Rotational analysis gave the B values for the combining states, and by fixing the CF bond lengths at ab initio values we obtained r″Si–C=1.6921Å and r′Si–C=1.594(1)Å. The bond lengths correspond to a silicon-carbon double bond in the ground state and an unusual Si−C triple bond in the excited state. Single vibronic level emission spectra yielded the ground state bending and stretching energy levels. These were fitted to a Renner-Teller model that included spin-orbit and limited vibrational anharmonicity effects.
Marine and coastal conservation: a rising affair
Authors: Dittmann Sabine
Published: July 2018

Conservation of coastal and marine ecosystems is in growing demand globally, as cumulative impacts are threatening the function and services provided by these ecosystems. This perspective provides recent insight into some of the pressures and developments in research and policy pertaining to coastal and marine conservation and restoration. A personal reflection on a pathway in conservation science is included to entice young scientists to embark on their journey for a future career in conservation science.
Transient surface ocean oxygenation recorded in the ∼2.66-Ga Jeerinah Formation, Australia
Authors: Koehler Matthew C. , Buick Roger , Kipp Michael A. , Stüeken Eva E. , Zaloumis Jonathan
Published: July 2018

Significance

Understanding how and when Earth’s surface became oxygenated is essential for understanding its biogeochemical evolution. Incipient oxygenation of Earth’s surface environments before the Great Oxidation Event (GOE; ∼2.4 Ga) has been well-documented, but the nature of these redox changes, whether protracted or transient, is poorly understood. We present nitrogen isotope ratios, selenium abundances, and selenium isotope ratios from the Jeerinah Formation (∼2.66 Ga; Fortescue Group, Western Australia) that represent (i) high-resolution evidence of transient surface ocean oxygenation ∼260 My before the GOE, (ii) a possible muted pulse of oxidative continental weathering, and (iii) the oldest firm evidence for nitrification and denitrification metabolisms. These results, in concert with previous studies, highlight the variability in mechanisms and magnitudes of Neoarchean oxygen fluctuations.
Estrogen-regulated feedback loop limits the efficacy of estrogen receptor–targeted breast cancer therapy
Authors: Xiao Tengfei , Li Wei , Wang Xiaoqing , Xu Han , Yang Jixin , Wu Qiu , Huang Ying , Geradts Joseph , Jiang Peng , Fei Teng , Chi David , Zang Chongzhi , Liao Qi , Rennhack Jonathan , Andrechek Eran , Li Nanlin , Detre Simone , Dowsett Mitchell , Jeselsohn Rinath M. , Liu X. Shirley , Brown Myles
Published: July 2018

Significance

Estrogen receptor-positive (ER
+
) breast cancer is treated with endocrine therapies, although therapeutic resistance almost invariably develops in advanced disease. Using genome-wide CRISPR screens, we identified genes whose loss confers endocrine resistance, as well as synthetic lethal vulnerabilities to overcome such resistance. These findings reveal an estrogen-induced negative feedback loop that constrains the growth of ER
+
tumors, thereby limiting the efficacy of therapies that inhibit ER, and suggest a previously unappreciated therapeutic route to overcoming endocrine resistance.
Ancient drug curcumin impedes 26S proteasome activity by direct inhibition of dual-specificity tyrosine-regulated kinase 2
Authors: Banerjee Sourav , Ji Chenggong , Mayfield Joshua E. , Goel Apollina , Xiao Junyu , Dixon Jack E. , Guo Xing
Published: July 2018

Significance

Curcumin is an ancient drug derived from turmeric and has been found to exhibit potent anticancer properties albeit through controversial mechanisms of action. Using a biochemical model, mouse cancer model, and cellular models, we show that curcumin is a highly potent and selective inhibitor of dual-specificity tyrosine-regulated kinase 2 (DYRK2), a positive regulator of the 26S proteasome. Curcumin perturbs 26S proteasome activity via DYRK2 inhibition in various cancer cells and in the mouse cancer model leading to impairment of cell proliferation and reduction of cancer burden in mice. This novel mechanism of action of curcumin opens up new avenues for potential preventative or therapeutic strategies in proteasome-addicted cancers like triple-negative breast cancer and multiple myeloma.
Between invisibility and over-visibility
Authors: Zheng Binghan , Xiang Xia
Published: July 2018

Recent research on liaison interpreting shows that the interpreters’ role in communicative events includes language facilitator and
intercultural mediator. Being empowered with more coordinating functions rather than regarded as invisible conduits, however, how
do interpreters with different professional experiences perceive their own role in business settings? And what are the actual
expectations on them from their clients? This paper tries to answer the questions through a questionnaire-based survey of three
groups of respondents: professional interpreters, student interpreters and clients, with each group including 30 respondents.
Chesterman’s (2001) four models of ethics, together with the hypothetical no ethics
model, were designed as answers to the questionnaire (17 closed questions) and translation versions to two interpreting samples.
The frequencies of responses to the questions and the evaluation scores of the translation versions are collected and analyzed,
revealing the following findings: All three groups acknowledge the constraints translation ethics place on the freedom of action;
and all three groups agree that interpreters simultaneously shoulder the tasks of translating and coordinating, with the “ethics
of communication” being the most widely acknowledged one. However, there are discrepancies between and within the groups, and even
attitudinal inconsistencies and contradictions in individual participants. These findings, by re-describing the interpreter’s
power in interlingual and intercultural interactions, will help improve professional standards and interpreting training.
Evolutionary Phonology and the life cycle of voiceless
sonorants
Authors: Blevins Juliette
Published: July 2018

In this chapter I examine the phonetic origins of voiceless
sonorants cross-linguistically within the general framework of
Evolutionary Phonology (Blevins
2004; 2006;
2008b; 2015). In terms of a general
hierarchy of contrast, we observe that: voiceless obstruents are
common; voiceless sonorant consonants are uncommon; voiceless vowels
are extremely rare. One phonetic source of voiceless sonorants
is coarticulation in RH and HR and clusters, where R is a sonorant
and H is a segment produced with a spread glottal gesture. Voiceless
sonorants may also arise when laryngeal spreading gestures are
associated with prosodic domains. In this second case, voiceless
sonorants can arise as allophones of their voiced counterparts.
While a fair number of languages show voiceless sonorant glides,
liquids and nasals phonologized as a consequence  of RH/HR
coarticulation, voiceless vowels resist phonologization despite
their high frequency as phonetic variants of modal vowels. In
some cases, voiceless vowels are lost before phonologization can
occur. In other cases, resistance to phonologization may be due to
effects of analogy, /h/, word phonotactics, or lexical
competition.
From ergative case-marking to hierarchical agreement
Authors: Guillaume Antoine
Published: July 2018

This paper reconstructs the history of a set of innovated 1st and 2nd
person verbal prefixes in Reyesano which manifest the phenomenon of
‘hierarchical agreement’ in transitive clauses, according to a
2>1>3 hierarchy. I argue that these prefixes come from
independent ergative-absolutive pronouns which first became
case-neutral enclitics in 2nd position in main clauses and then verb
prefixes. And I show that the hierarchical effects that the prefixes
manifest in synchrony have nothing to do with the working of a
hierarchy during the grammaticalization process. In doing so, the
paper contributes to the growing body of diachronic evidence against
the idea that the person hierarchy is a universal of human language
reflecting a more general principal of human cognition.
Adding omega‐3 fatty acids to a protein‐based supplement during pre‐season training results in reduced muscle soreness and the better maintenance of explosive power in professional Rugby Union players
Authors: Black Katherine Elizabeth , Witard Oliver C. , Baker Dane , Healey Philip , Lewis Victoria , Tavares Francisco , Christensen Sam , Pease Tom , Smith Brett
Published: July 2018

Evidence suggests that omega‐3 fatty acid supplementation could reduce muscle soreness and maintain muscle function following eccentric exercise‐induced muscle damage. The aim of this applied field study was to investigate the effectiveness of consuming a protein‐based supplement containing 1546 mg of omega‐3 polyunsaturated fatty acid (PUFA) (551 mg eicosapentaenoic acid (EPA) and 551 mg docosahexaenoic acid (DHA)) twice daily (FO) compared to a protein‐based placebo (P) on muscle soreness, countermovement jump (CMJ) performance and psychological well‐being in 20 professional Rugby Union players during 5 weeks of pre‐season training. Players completed a 5‐point‐Likert soreness scale with 5 indicating “no soreness” and a questionnaire assessing fatigue, sleep, stress and mood each morning of training, plus they performed CMJ tests once or twice per week. Data were analysed using magnitude‐based inferential statistics and are presented as percent beneficial/trivial/harmful. On day 35, there was a likely (% beneficial/trivial/harmful: 94/5/1) moderate (0.75, standardized mean difference (SMD)) beneficial effect of FO vs. P on the change in lower body muscle soreness compared with day 0 (FO: −3.8 ± 21.7%; P: −19.4 ± 11.2%). There was a likely (92/7/0) moderate (SMD: 0.60) beneficial effect of FO vs. P on CMJ performance (change from baseline to day 35, FO: +4.6 ± 5.9%; P: −3.4 ± 8.6%). From day 20, a moderate beneficial effect of FO on fatigue was observed. In terms of practical relevance, the moderate beneficial effect of adding fish oil to a protein‐based supplement on muscle soreness translated into the better maintenance of explosive power in elite Rugby Union players during pre‐season training.
Care Home Life and Identity: A Qualitative Case Study
Authors: Paddock Katie , Brown Wilson Christine , Walshe Catherine , Todd Chris
Published: July 2018

Background and Objectives

The transition to a care home can involve multiple changes and losses that can affect an older person’s well-being and identity. It is not clear how older people perceive and manage their identity within a care home over time. This study explores how living in a care home affects the identities of residents and how they address this in their daily lives.

Research Design and Methods

A multiple qualitative case study approach incorporated interview and observational data. Eighteen semistructured interviews and 260 hr of observations were conducted over 1 year with care home residents, relatives, and staff across three care homes within Greater Manchester, UK. Data were analyzed using framework analysis, drawing on the social identity perspective as an interpretive lens.

Results

Four themes were identified: (a) changing with age, (b) independence and autonomy, (c) bounded identity, and (d) social comparison. The impact of aging that initially altered residents’ identities was exacerbated by the care home environment. Institutional restrictions jeopardized independence and autonomy, provoking residents to redefine this within the allowances of the care home. Strict routines and resource constraints of well-meaning staff resulted in the bounded expression of personalities. Consequently, to forge a positive identity, residents without dementia engaged in social comparison with residents with dementia, emphasizing their superior cognitive and physical abilities.

Discussion and Implications

Social comparison as an adaptive strategy has previously been unidentified in care home literature. Residents need more support to express their identities, which may reduce the necessity of social comparison, and improve interrelationships and well-being.
Failures in reproductive health policy: overcoming the consequences and causes of inaction
Authors: Sher Jonathan , Frank John W , Doi Lawrence , de Caestecker Linda
Published: July 2018

It is assumed that long-established research findings and internationally accepted evidence should, and will, be translated into policy and practice. Knowledge about what prevents harm and promotes health has, in fact, guided and resulted in numerous beneficial public health actions. However, such is not always the case. The authors examine three notable, and unwelcome, exceptions in the UK—all in the field of reproductive health and all focused on the period prior to pregnancy. The three examples of counterproductive inaction discussed are: fortifying flour with Vitamin B9 (folic acid); preventing foetal alcohol spectrum disorders; and reducing risks and better regulating a highly teratogenic medication (valproate). The adverse consequences, as well as the causes, of inaction are analysed for each example. Reasons for optimism, and recommendations for overcoming inaction, are also offered, in particular, greater priority should be accorded to preconception health, education and care.
Aquatic caddisworm silk is solidified by environmental metal ions during the natural fiber‐spinning process
Authors: Ashton Nicholas N. , Stewart Russell J.
Published: July 2018

Aquatic caddisfly larvae (caddisworms) wet‐spin fibers to construct composite cases of silk and stone. The silk emerges from labial ducts as a nanofibrous fluid gel, flowing over the stone substrate and making intimate interfacial adhesive contacts before being drawn into tough fibers that rapidly solidify underwater to span gaps in the construction. Divalent metal ions are responsible for the unique mechanical properties of naturally spun silk fibers; however, when and where divalent metal ions are incorporated into the metallofibers and other aspects of the fiber solidification mechanism are poorly understood. To investigate, the elemental composition and secondary structure of silk precursors stored in the silk gland lumen were compared with naturally spun fibers by inductively coupled plasma optical emission spectroscopy and attenuated total reflection Fourier transform infrared spectroscopy. Naturally spun fibers contained near equimolar ratios of Ca2+ to P. In contrast, silk precursors stored in the silk gland lumen contained only traces of Ca2+ and other multivalent metal ions. Ca2+ was also undetectable in anterior lumenal silk using the histochemical Ca2+ indicator, alizarin S red. Addition of Ca2+ to isolated lumenal silk resulted in Ca2+ complexation by H‐fibroin phosphoserines (pSs) and a shift in secondary structure from random coils to β‐structures, creating infrared spectra in the phosphate and amide I regions nearly equivalent to those found in naturally spun Ca2+‐containing silk fibers. Light and electron microscopy within distinct regions of the silk gland suggested that posterior gland silk colloidal complexes transition into a nanofibrous morphology as they pass into the chitin‐lined anterior lumen. Altogether, the results suggest that environmental Ca2+ absorbed from natural water triggers silk fiber solidification postdraw by complexing H‐fibroin pSs, creating Ca2+‐stabilized crystalline β‐nanodomains that cross‐link and toughen the freshly drawn silk fibers.—Ashton, N. N., Stewart, R. J. Aquatic caddisworm silk is solidified by environmental metal ions during the natural fiber‐spinning process. FASEB J. 33, 572–583 (2019). www.fasebj.org
Quantitative Apparent Diffusion Coefficient Derived From Diffusion-Weighted Imaging Has the Potential to Avoid Unnecessary MRI-Guided Biopsies of mpMRI-Detected PI-RADS 4 and 5 Lesions
Authors: Polanec Stephan H. , Helbich Thomas H. , Bickel Hubert , Wengert Georg J. , Pinker Katja , Spick Claudio , Clauser Paola , Susani Martin , Shariat Shahrokh , Baltzer Pascal A.T.
Published: July 2018

Objective

The aim of this study was to evaluate the potential of diffusion-weighted imaging–derived apparent diffusion coefficient (ADC) measurements to obviate unnecessary biopsies in multiparametric MRI–detected PI-RADS 4 and 5 lesions.

Materials and Methods

This retrospective, institutional review board–approved study investigated 101 PI-RADS 4 and 5 prostate lesions (52 malignant, 49 benign) verified by in-bore MRI-guided biopsy in 101 men (mean age, 62.8 years). Two readers, who were not aware of the biopsy results independently and repeatedly measured minimum, mean, and maximum ADC from diffusion-weighted imaging measurements (in line with PI-RADS v2 recommendations) using a 2-dimensional region of interest drawn around the biopsied lesions. Diagnostic performance was evaluated using receiver operating characteristic statistics and reproducibility statistics were calculated.

Results

The best diagnostic performance (overall area under the receiver operating characteristic curve [AUC] R1: 0.801; R2: 0.796 peripheral zone AUC R1:0.814, R2: 0.805; transitional zone AUC R1:0.786, R2:0.779) and the tightest limits of interreader agreement (−8.6% to 9.9%) were found in minimum ADC values. Rule-in and rule-out thresholds for diagnosis of prostate cancer were identified, demonstrating a potential to avoid unnecessary biopsies in 32.7% (16/49).

Conclusions

Quantitative ADC measurement in multiparametric MRI–detected PI-RADS 4 and 5 lesions has the potential to avoid unnecessary MRI-guided biopsies in up to 33%.
On the use of wavelets to reveal oscillatory patterns in stellar flare emission
Authors: López-Santiago J.
Published: July 2018

Wavelet analysis is a powerful tool to investigate non-stationary signals such as amplitude modulated sinusoids or single events lasting for a small percentage of the observing time. Wavelet analysis can be used, for example, to reveal oscillations in the light curve of stars during coronal flares. A careful treatment of the background in the wavelet scalogram is necessary to determine robust confidence levels required to distinguish between patterns caused by actual oscillations and noise. This work describes the method using synthetic light curves and investigates the effect of background noise when determining confidence levels in the scalogram. The result of this analysis shows that the wavelet transform is able to reveal oscillatory patterns even when frequency-dependent noise is dominant. However, their significance in the wavelet scalogram may be reduced, depending on the assumed background spectrum. To show the power of wavelet analysis, the light curve of a well-known flaring star is analysed. It shows two oscillations overlapped. The lower-frequency oscillation is not mentioned in previous works in the literature. This result demonstrates the need for correctly characterizing the background noise of the signal.

This article is part of the theme issue ‘Redundancy rules: the continuous wavelet transform comes of age’.
Analysis of time-varying signals using continuous wavelet and synchrosqueezed transforms
Authors: Tary Jean Baptiste , Herrera Roberto Henry , van der Baan Mirko
Published: July 2018

The continuous wavelet transform (CWT) has played a key role in the analysis of time-frequency information in many different fields of science and engineering. It builds on the classical short-time Fourier transform but allows for variable time-frequency resolution. Yet, interpretation of the resulting spectral decomposition is often hindered by smearing and leakage of individual frequency components. Computation of instantaneous frequencies, combined by frequency reassignment, may then be applied by highly localized techniques, such as the synchrosqueezing transform and ConceFT, in order to reduce these effects. In this paper, we present the synchrosqueezing transform together with the CWT and illustrate their relative performances using four signals from different fields, namely the LIGO signal showing gravitational waves, a ‘FanQuake’ signal displaying observed vibrations during an American football game, a seismic recording of the
M

w

8.2 Chiapas earthquake, Mexico, of 8 September 2017, followed by the Irma hurricane, and a volcano-seismic signal recorded at the Popocatépetl volcano showing a tremor followed by harmonic resonances. These examples illustrate how high-localization techniques improve analysis of the time-frequency information of time-varying signals.

This article is part of the theme issue ‘Redundancy rules: the continuous wavelet transform comes of age’.
Nonlinear analysis of natural folds using wavelet transforms and recurrence plots
Authors: Ord Alison , Hobbs Bruce , Dering Greg , Gessner Klaus
Published: July 2018

Three-dimensional models of natural geological fold systems established by photogrammetry are quantified in order to constrain the processes responsible for their formation. The folds are treated as nonlinear dynamical systems and the quantification is based on the two features that characterize such systems, namely their multifractal geometry and recurrence quantification. The multifractal spectrum is established using wavelet transforms and the wavelet transform modulus maxima method, the generalized fractal or Renyi dimensions and the Hurst exponents for longitudinal and orthogonal sections of the folds. Recurrence is established through recurrence quantification analysis (RQA). We not only examine natural folds but also compare their signals with synthetic signals comprising periodic patterns with superimposed noise, and quasi-periodic and chaotic signals. These results indicate that the natural fold systems analysed resemble periodic signals with superimposed chaotic signals consistent with the nonlinear dynamical theory of folding. Prediction based on nonlinear dynamics, in this case through RQA, takes into account the full mechanics of the formation of the geological system.

This article is part of the theme issue ‘Redundancy rules: the continuous wavelet transform comes of age’.
The Stress-Chip: A microfluidic platform for stress analysis inCaenorhabditis elegans
Authors: Banse Stephen A. , Blue Benjamin W. , Robinson Kristin J. , Jarrett Cody M. , Phillips Patrick C.
Published: July 2018

An organism’s ability to mount a physiological response to external stressors is fundamental to its interaction with the environment. Experimental exploration of these interactions benefits greatly from the ability to maintain tight control of the environment, even under conditions in which it would be normal for the subject to flee the stressor. ere we present a nematode research platform that pairs automated image acquisition and analysis with a custom microfluidic device. This platform enables tight environmental control in low-density, single-worm arenas, which preclude animal escape while still allowing a broad range of behavioral activities. The platform is easily scalable, with two 50 arena arrays per chip and an imaging capacity of 600 animals per scanning device. Validating the device using dietary, osmotic, and oxidative stress indicates that it should be of broad use as a research platform, including eventual adaptation for additional stressors, anthelmintic-drug screening, and toxicology studies.
Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome
Authors: Keeble-Gagnère G. , Rigault P. , Tibbits J. , Pasam R. , Hayden M. , Forrest K. , Frenkel Z. , Korol A. , Huang E. , Cavanagh C. , Taylor J. , Abrouk M. , Sharpe A. , Konkin D. , Sourdille P. , Darrier B. , Choulet F. , Bernard A. , Rochfort S. , Dimech AM. , Watson-Haigh N. , Baumann U. , Eckermann P. , Fleury D. , Juhasz A. , Boisvert S. , Nolin M-A. , Doležel J. , Šimková H. , Toegelová H. , Šafář Jan , Luo M-C. , Camara F. , Pfeifer M. , Isdale D. , Nystrom-Persson J. ,   IWGSC, Koo D-H , Tinning M. , Cui D. , Ru Z. , Appels R.
Published: July 2018

Background

Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome.

Results

Using chromosome 7A of wheat as a model, sequence-finished megabase scale sections of this chromosome were established by combining a new independent assembly based on a BAC-based physical map, BAC pool paired end sequencing, chromosome arm specific mate-pair sequencing and Bionano optical mapping with the IWGSC RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region.

Conclusions

Sufficient genome sequence information is shown to be now available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and yield attributes are affected by five f-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.
PIK3C2Bpromotes epithelial to mesenchymal transition and EGFR inhibitors insensitivity in epidermal squamous cell carcinoma
Authors: Pomar Silvia Crespo , Borgström Anna , Arcaro Alexandre , Charles Roch-Philippe
Published: July 2018

While the class I of PI3Ks has been deeply studied due to its clear implication in cancer development, little is known about the class II of PI3Ks. However, recent accumulation of data is now revealing that PI3KC2β, one isoform of this class of PI3Ks, may also play a role in cancer. Specifically, recent studies have suggested an implication of PI3KC2β in metastasis formation through the promotion of epithelial to mesenchymal transition (EMT). Here, we report that the overexpression of PI3KC2β in the epidermal squamous cell carcinoma (ESCC) cells A431 promotes apparent EMT transformation. We further confirm this EMT by showing modification in several biochemical markers (E-cadherin, β-catenin, Snail, Twist1 and Vimentin). Furthermore, an intracellular co-localization of E-cadherin, β-catenin and EGFR was observed. This transformation decreased EGFR signaling and the sensitivity to inhibitors targeting this receptor. To confirm our results, we have used the colon adenocarcinoma cells HT29 and induced overexpression of PI3KC2β in these cells. We could recapitulate in this model some of our major findings regarding EMT in the PI3KC2β overexpressing A431 cells. Taken together, these data support a role of PI3KC2β in promoting EMT.
Scoring of pathogenic non-coding variants in Mendelian diseases through supervised learning on ancient, recent and ongoing purifying selection signals in human
Authors: Caron Barthélémy , Luo Yufei , Rausell Antonio
Published: July 2018

The study of rare Mendelian diseases through exome sequencing typically yields incomplete diagnostic rates, ~8-70% depending on the disease type. Whole genome sequencing of the unresolved cases allows addressing the hypothesis that causal variants could lay in non-coding regions with damaging regulatory consequences. The large amount of rare and singleton variants found in each individual genome requires computational filtering and scoring strategies to gain power in downstream statistical genetics tests. However, state-of-the-art methods estimating the functional relevance of non-coding genomic regions have been mostly characterized on sets of variants largely composed of trait-associated polymorphisms and associated to common diseases, yet with modest accuracy and strong positional biases. In this work we first curated a collection of n=737 high-confidence pathogenic non-coding single-nucleotide variants in proximalcis-regulatory genomic regions associated to monogenic Mendelian diseases. We then systematically evaluated the ability to predict causal variants of a comprehensive set of natural selection features extracted at three genomic levels: the affected position, the flanking region and the associated gene. In addition to inter-species conservation, a comprehensive set of recent and ongoing purifying selection signals in human was explored, allowing to capture potential constraints associated to recently acquired regulatory elements in the human lineage. A supervised learning approach using gradient tree boosting on such features reached a high predictive performance characterized by an area under the ROC curve = 0.84 and an area under the Precision-Recall curve = 0.47. The figures represent a relative improvement of >10% and >34% respectively upon the performance of current state-of-the-art methods for prioritizing non-coding variants. Performance was consistent under multiple configurations of the sets of variants used for learning and for independent testing. The supervised learning design allowed the assessment of newly seen non-coding variants overcoming gene and positional bias. The scores produced by the approach allow a more consistent weighting and aggregation of candidate pathogenic variants from diverse non-coding regions within and across genes in the context of statistical tests for rare variant association analysis.
Lineage tracing of Notch1-expressing cells in intestinal tumours reveals a distinct population of cancer stem cells
Authors: Mourao Larissa , Jacquemin Guillaume , Huyghe Mathilde , Nawrocki Wojciech J. , Menssouri Naoual , Servant Nicolas , Fre Silvia
Published: July 2018

Colon tumours are hierarchically organized and contain multipotent self-renewing cells, called Cancer Stem Cells (CSCs). We have previously shown that the Notch1 receptor is expressed in Intestinal Stem Cells (ISCs); given the critical role played by Notch signalling in promoting intestinal tumourigenesis, we explored Notch1 expression in tumours. Combining lineage tracing in two tumour models with transcriptomic analyses, we found that Notch1 + tumour cells are undifferentiated, proliferative and capable of indefinite self-renewal and of generating a heterogeneous clonal progeny. Molecularly, the transcriptional signature of Notch1+ tumour cells highly correlates with ISCs, suggestive of their origin from normal crypt cells. Surprisingly, Notch1+ expression labels a subset of CSCs that show reduced levels of Lgr5, a reported CSCs marker. The existence of distinct stem cell populations within intestinal tumours highlights the necessity of better understanding their hierarchy and behaviour, to identify the correct cellular targets for therapy.
CancerMine: A literature-mined resource for drivers, oncogenes and tumor suppressors in cancer
Authors: Lever Jake , Zhao Eric Y. , Grewal Jasleen , Jones Martin R. , Jones Steven J. M.
Published: July 2018

Understanding a mutation in cancer requires knowledge of the different roles that genes play in cancer as drivers, oncogenes and tumor suppressors. We present CancerMine, a high-quality text-mined knowledgebase that catalogues over 856 genes as drivers, 2,421 as oncogenes and 2,037 as tumor suppressors in 426 cancer types. We compile 3,485 genes that are not in the IntOGen resource of drivers and complement the Cancer Gene Census with 3,136 new genes identified as oncogenes and tumor suppressors. CancerMine provides a method for gene-centric clustering of cancer types illustrating genetic similarities between cancer types of different organs and was validated against data from the Cancer Genome Atlas (TCGA) project. Finally with 178 novel cancer gene mentions in publications each month, this resource will be updated monthly, pre-empting the need to manually curate the ever-increasing number of novel cancer associated genes. CancerMine is viewable through a web portal (http://bionlp.bcgsc.ca/cancermine/) and available for download (https://github.com/jakelever/cancermine).
Factors Related to Dental Caries, Periodontal Disease, and Psychological effect of those diseases: A Structural Equation Modeling and Artificial Neural Network model comparative approach
Authors: Ghosh Capt Sirsendu
Published: July 2018

Exceptional growth in the development of oral health of various populations worldwide over the last three decades cannot lessen tribulations in dental caries, periodontal disease, and psychological problems, which are still prevalent in many communities, especially among the poor socioeconomic groups in developing countries like India. Dental caries and periodontal disease are exceedingly related to the lifestyle associated risk factors and various daily habits including smoking and tobacco chewing. Dietary habit is one of the prime causative behind the formation of dental caries and simultaneously the dietary habit is greatly influenced by the person’s socio-economic status. In this study to explore the factors related to dental caries and periodontal disease and how these diseases manipulate the mental health of the people, some SEMs and some ANN models are also formed. At last both models are compared and explained about their purposes and usability for further applications.
pymfinder: a tool for the motif analysis of binary and quantitative complex networks
Authors: Mora Bernat Bramon , Cirtwill Alyssa R. , Stouffer Daniel B.
Published: July 2018

We developed pymfinder, a new software to analyze multiple aspects of the so-called network motifs—distinct n-node patterns of interaction—for any directed, undirected, unipartite or bipartite network. Unlike existing software for the study of network motifs, pymfinder allows the computation of node- and link-specific motif profiles as well as the analysis of weighted motifs. Beyond the overall characterization of networks, the tools presented in this work therefore allow for the comparison of the “roles” of either nodes or links of a network. Examples include the study of the roles of different species and/or their trophic/mutualistic interactions in ecological networks or the roles of specific proteins and/or their activation/inhibition relationships in protein-protein interaction networks. Here, we show how to apply the main tools from pymfinder using a predator-prey interaction network from a marine food web. pymfinder is open source software that can be freely and anonymously downloaded from https://github.com/stoufferlab/pymfinder, distributed under the MIT License (2018).
Comprehensive transcriptional profiling of the gastrointestinal tract of ruminants from birth to adulthood reveals strong developmental stage specific gene expression
Authors: Bush S. J. , McCulloch M. E. B. , Muriuki C. , Salavati M. , Davis G. M. , Farquhar I. L. , Lisowski Z. M. , Archibald A. L. , Hume D. A. , Clark E. L.
Published: July 2018

One of the most significant physiological challenges to neonatal and juvenile ruminants is the development and establishment of the rumen. Using a subset of RNA-Seq data from our high-resolution atlas of gene expression in sheep (Ovis aries) we have provided the first comprehensive characterisation of transcription of the entire the gastrointestinal (GI) tract during the transition from pre-ruminant to ruminant. The dataset comprises 168 tissue samples from sheep at four different time points (birth, one week, 8 weeks and adult). Using network cluster analysis we illustrate how the complexity of the GI tract is reflected in tissue- and developmental stage-specific differences in gene expression. The most significant transcriptional differences between neonatal and adult sheep were observed in the rumen complex. Differences in transcription between neonatal and adult sheep were particularly evident in macrophage specific signatures indicating they might be driving the observed developmental stage-specific differences. Comparative analysis of gene expression in three GI tract tissues from age-matched sheep and goats revealed species-specific differences in genes involved in immunity and metabolism. This study improves our understanding of the transcriptomic mechanisms involved in the transition from pre-ruminant to ruminant. It highlights key genes involved in immunity, microbe recognition, metabolism and cellular differentiation in the GI tract. The results form a basis for future studies linking gene expression with microbial colonisation of the developing GI tract and will contribute towards identifying genes that underlie immunity in early development, which could be utilised to improve ruminant efficiency and productivity.

Reference Numbers for Data in the Public Repositories

The raw RNA-Sequencing data are deposited in the European Nucleotide Archive (ENA) under study accessions PRJEB19199 (sheep) and PRJEB23196 (goat). Metadata for all samples is deposited in the EBI BioSamples database under group identifiers SAMEG317052 (sheep) and SAMEG330351 (goat).
Expression and role of Galectin-3 in the postnatal development of the cerebellum
Authors: González-Calvo Inés , Selimi Fekrije
Published: July 2018

Many proteins initially identified in the immune system play roles in neurogenesis, neuronal migration, axon guidance, synaptic plasticity and other processes related to the formation and refinement of neural circuits. Although the function of the immune-related protein Galectin-3 (LGALS3) has been extensively studied in the regulation of inflammation, cancer and microglia activation, little is known about its role in the development of the brain. In this study, we identified that LGALS3 is expressed in the developing postnatal cerebellum. More precisely, LGALS3 is expressed by cells in meninges and in the choroid plexus, and in subpopulations of astrocytes and of microglial cells in the cerebellar cortex. Analysis ofLgals3knockout mice showed thatLgals3is dispensable for the development of cerebellar cytoarchitecture and Purkinje cell excitatory synaptogenesis in the mouse.
Alternative (backdoor) androgen production and masculinization in the human fetus
Authors: O’Shaughnessy Peter J , Antignac Jean Philippe , Bizec Bruno Le , Morvan Marie-Line , Svechnikov Konstantin , Söder Olle , Savchuk Iuliia , Monteiro Ana , Soffientini Ugo , Johnston Zoe C , Bellingham Michelle , Hough Denise , Bhattacharya Siladitya , Walker Natasha , Filis Panagiotis , Fowler Paul A
Published: July 2018

Masculinization of the external genitalia in humans is dependent on formation of 5α-dihydrotestosterone (DHT) through both the canonical androgenic pathway and an alternative (backdoor) pathway. The fetal testes are essential for canonical androgen production but little is known about the synthesis of backdoor androgens despite their known critical role in masculinization. In this study, we have measured plasma and tissue levels of endogenous steroids in second trimester human male fetuses using multi-dimensional and high-resolution mass-spectrometry. Results show that androsterone is the principal backdoor androgen in the fetal circulation and that DHT is undetectable (<1ng/ml). Backdoor pathway intermediates are found primarily in the placenta and fetal liver with significant androsterone levels also in the fetal adrenal. Backdoor intermediates, including androsterone, are mostly undetectable in the fetal testes. This is consistent with transcript levels of enzymes involved in the backdoor pathway (SRD5A1, AKR1C2/4, CYP17A1), as measured by qPCR. These data identify androsterone as the predominant backdoor androgen in the human fetus and show that it is formed primarily in non-gonadal tissue with placental progesterone the likely substrate. Masculinization of the human fetus depends, therefore, on androgen synthesis by both the fetal testes and non-gonadal tissues leading to DHT formation at the genital tubercle. Our findings provide, for the first time, a solid basis to explain why placental insufficiency is associated with disorders of sex development in humans
Inferring the presence of aflatoxin-producingAspergillus flavusstrains using RNA sequencing and electronic probes as a transcriptomic screening tool
Authors: Espindola Andres S. , Schneider William , Cardwell Kitty F. , Carrillo Yisel , Hoyt Peter R. , Marek Stephen M. , Melouk Hassan , Garzon Carla D.
Published: July 2018

E-probe Diagnostic for Nucleic acid Analysis (EDNA) is a bioinformatic tool originally developed to detect plant pathogens in metagenomic databases. However, enhancements made to EDNA increased its capacity to conduct hypothesis directed detection of specific gene targets present in transcriptomic databases. To target specific pathogenicity factors used by the pathogen to infect its host or other targets of interest, e-probes need to be developed for transcripts related to that function. In this study, EDNA transcriptomics (EDNAtran) was developed to detect the expression of genes related to aflatoxin production at the transcriptomic level. E-probes were designed from genes up-regulated duringA.flavusaflatoxin production. EDNAtran detected gene transcripts related to aflatoxin production in a transcriptomic database from corn, where aflatoxin was produced. The results were significantly different from e-probes being used in the transcriptomic database where aflatoxin was not produced (atoxigenic AF36 strain and toxigenic AF70 in Potato Dextrose Broth).