bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of phonons in negative thermal expansion and high pressure phase transitions in β-eucryptite: An ab-initio lattice dynamics and inelastic neutron scattering study
Authors: Singh Baltej , Gupta Mayanak Kumar , Mittal Ranjan , Zbiri Mohamed , Rols Stephane , Patwe Sadequa Jahedkhan , Achary Srungarpu Nagabhusan , Schober Helmut , Tyagi Avesh Kumar , Chaplot Samrath Lal
Published: March 2017

β-Eucryptite (LiAlSiO4) shows anisotropic thermal expansion as well as one-dimensional super-ionic conductivity. We have performed the lattice dynamical calculations using ab-initio density functional theory along with inelastic neutron scattering measurements. The anisotropic stress dependence of the phonon spectrum is calculated to obtain the thermal expansion behavior along various axes. The calculations show that the Grüneisen parameters of the low-energy phonon modes around 10 meV have large negative values and govern the negative thermal expansion behavior at low temperatures along both the “a”- and “c”-axes. On the other hand, anisotropic elasticity along with anisotropic positive values of the Grüneisen parameters of the high-energy modes in the range 30–70 meV are responsible for the thermal expansion at high temperatures, which is positive in the a-b plane and negative along the c-axis. The analysis of the polarization vectors of the phonon modes sheds light on the mechanism of the anomalous thermal expansion behavior. The softening of a Γ-point mode at about 2 GPa may be related to the high-pressure phase transition.
How Markovian is exciton dynamics in purple bacteria?
Authors: Vaughan Felix , Linden Noah , Manby Frederick R.
Published: March 2017

We investigate the extent to which the dynamics of excitons in the light-harvesting complex LH2 of purple bacteria can be described using a Markovian approximation. To analyse the degree of non-Markovianity in these systems, we introduce a measure based on fitting Lindblad dynamics, as well as employing a recently introduced trace-distance measure. We apply these measures to a chromophore-dimer model of exciton dynamics and use the hierarchical equation-of-motion method to take into account the broad, low-frequency phonon bath. With a smooth phonon bath, small amounts of non-Markovianity are present according to the trace-distance measure, but the dynamics is poorly described by a Lindblad master equation unless the excitonic dimer coupling strength is modified. Inclusion of underdamped, high-frequency modes leads to significant deviations from Markovian evolution in both measures. In particular, we find that modes that are nearly resonant with gaps in the excitonic spectrum produce dynamics that deviate most strongly from the Lindblad approximation, despite the trace distance measuring larger amounts of non-Markovianity for higher frequency modes. Overall we find that the detailed structure in the high-frequency region of the spectral density has a significant impact on the nature of the dynamics of excitons.
Large-time limit of the quantum Zeno effect
Authors: Facchi Paolo , Ligabò Marilena
Published: March 2017

If very frequent periodic measurements ascertain whether a quantum system is still in its initial state, its evolution is hindered. This peculiar phenomenon is called quantum Zeno effect. We investigate the large-time limit of the survival probability as the total observation time scales as a power of the measurement frequency, t∝Nα. The limit survival probability exhibits a sudden jump from 1 to 0 at α=1/2, the threshold between the quantum Zeno effect and a diffusive behavior. Moreover, we show that for α≥1, the limit probability becomes sensitive to the spectral properties of the initial state and to the arithmetic properties of the measurement periods.
Multi-piecewise quadratic nonlinearity memristor and its 2N-scroll and 2N + 1-scroll chaotic attractors system
Authors: Wang Chunhua , Liu Xiaoming , Xia Hu
Published: March 2017

In this paper, two kinds of novel ideal active flux-controlled smooth multi-piecewise quadratic nonlinearity memristors with multi-piecewise continuous memductance function are presented. The pinched hysteresis loop characteristics of the two memristor models are verified by building a memristor emulator circuit. Using the two memristor models establish a new memristive multi-scroll Chua's circuit, which can generate 2N-scroll and 2N+1-scroll chaotic attractors without any other ordinary nonlinear function. Furthermore, coexisting multi-scroll chaotic attractors are found in the proposed memristive multi-scroll Chua's circuit. Phase portraits, Lyapunov exponents, bifurcation diagrams, and equilibrium point analysis have been used to research the basic dynamics of the memristive multi-scroll Chua's circuit. The consistency of circuit implementation and numerical simulation verifies the effectiveness of the system design.
Nitrogen chemical state in N-doped Cu2O thin films
Authors: Wang Y. , Ghanbaja J. , Horwat D. , Yu L. , Pierson J. F.
Published: March 2017

Nitrogen-doped Cu2O thin films have been deposited at room temperature by reactive magnetron sputtering. It is demonstrated that nitrogen doping in Cu2O can significantly improve the electrical properties by increasing the carrier concentration. The nitrogen chemical state in doped thin films has been investigated by electron energy loss spectroscopy, which reveals that nitrogen is in the form of molecular N2 in Cu2O thin films rather than the N-anion. Such experimental results are well consistent with the recently reported calculation, suggesting that in N-doped Cu2O, nitrogen mainly substitutes Cu in the molecular form, (N2)Cu, rather than in the atomic form at the oxygen site (NO).
Effect of density modulation on backward stimulated Raman Scattering in a laser-irradiated plasma
Authors: Zhang H. C. , Xiao C. Z. , Wang Q. , Feng Q. S. , Liu Z. J. , Zheng C. Y.
Published: March 2017

The influence of an arbitrary static sinusoidal density modulation on Raman backscattering is discussed theoretically and numerically. One-dimensional Vlasov simulations show a suppression of convective gain of seed with large modulation amplitude ϵ or small modulation vector ks, which is consistent with the modulation theory, namely, the generation of harmonics. However, this initial suppression is soon replaced by a periodic enhancement of reflectivity in the nonlinear stage due to the different performance of Langmuir wave propagation in density peaks and valleys. Modulation effects are also instantiated in electron acceleration. With large ks, finite orders of harmonics may lead to obvious layers of the phase island structure, and local phase island mixing occurs when the wave amplitude increases. With small ks, electrons could be accelerated by a series of adjacent harmonics from low phase velocity to high phase velocity step by step, which may produce a large number of superthermal electrons even with relativistic kinetic energy.
Crystalline silicon surface passivation by thermal ALD deposited Al doped ZnO thin films
Authors: Panigrahi Jagannath , Vandana  , Singh Rajbir , Rauthan C. M. S. , Singh P. K.
Published: March 2017

The evidence of good quality silicon surface passivation using thermal ALD deposited Al doped zinc oxide (AZO) thin films is demonstrated. AZO films are prepared by introducing aluminium precursor in between zinc and oxygen precursors during the deposition. The formation of AZO is confirmed by ellipsometry, XRD and Hall measurements. Effective minority carrier lifetime (τeff) greater than 1.5ms at intermediate bulk injection levels is realized for symmetrically passivated p-type silicon surfaces under optimised annealing conditions of temperature and time in hydrogen ambient. The best results are realised at 450°C annealing for >15min. Such a layer may lead to implied open circuit voltage gain of 80mV.
Nitrogen×sulfur interaction on fertiliser-use efficiency in bread wheat genotypes from the Argentine Pampas
Authors: Arata Agustin F. , Lerner Silvia E. , Tranquilli Gabriela E. , Arrigoni Adriana C. , Rondanini Deborah P.
Published: March 2017

Wheat crop response to sulfur (S) depends on nitrogen (N) level, genotype and environmental conditions, demonstrating strong genotype × environment × nutrients interactions. The agronomic-use efficiency of both nutrients has not been evaluated in a wide range of modern genotypes differing in their cycle length and baking quality. The aim of this study was to analyse the effect of N and S fertilisation on yield components and use efficiency of both nutrients in 24 modern, high-yielding bread wheat genotypes (including long and short crop cycles) grown in contrasting environments in the Humid Pampa of Argentina. Two experiments were conducted under contrasting seasonal conditions on a Mollisol in Azul, Buenos Aires. Significant effects of N (range 15–200 kg N ha–1) on grain yield were observed in all genotypes. By contrast, responses to S (30–100 kg S ha–1) were found only at high N level in low soil-fertility environments, differing between long and short cycles. Genotype × fertilisation interaction was significant in the environment with higher soil fertility. Sulfur addition improved N-recovery efficiency (0.15 v. 0.32) and agronomic efficiency of the available N (84 v. 93 g g–1) in the poor-fertility environment, characterised by their N and S deficiency and moderate level of organic matter. Grain N-recovery efficiency was largely explained by increases in grain number, whereas S recovery was also associated with increases in grain nutrient concentration. We conclude that genotype and environment strongly alter fertiliser-use efficiency, providing valuable information for ranking genotypes and optimising site-specific management of wheat crops in the Humid Pampa of Argentina. Grain S percentage may be useful as a physiological marker for selection of bread wheat genotypes with high apparent S recovery.
Why do plants lack sodium pumps and would they benefit from having one?
Authors: Pedersen Jesper T. , Palmgren Michael
Published: March 2017

The purpose of this minireview is to discuss the feasibility of creating a new generation of salt-tolerant plants that express Na+/K+-ATPases from animals or green algae. Attempts to generate salt-tolerant plants have focussed on increase the expression of or introducing salt stress-related genes from plants, bryophytes and yeast. Even though these approaches have resulted in plants with increased salt tolerance, plant growth is decreased under salt stress and often also under normal growth conditions. New strategies to increase salt tolerance are therefore needed. Theoretically, plants transformed with an animal-type Na+/K+-ATPase should not only display a high degree of salt tolerance but should also reduce the stress response exhibited by the first generation of salt-tolerant plants under both normal and salt stress conditions. The biological feasibility of such a strategy of producing transgenic plants that display improved growth on saline soil but are indistinguishable from wild-type plants under normal growth conditions, is discussed.
The Bramble Cay melomys Melomys rubicola (Rodentia : Muridae): a first mammalian extinction caused by human-induced climate change?
Authors: Waller Natalie L. , Gynther Ian C. , Freeman Alastair B. , Lavery Tyrone H. , Leung Luke K.-P.
Published: March 2017

Aims Sea-level rise is one of the most certain consequences of global warming and is predicted to exert significant adverse effects on wildlife in coastal habitats worldwide. Terrestrial fauna inhabiting low-lying islands are likely to suffer the greatest loss to habitat from sea-level rise and other oceanographic impacts stemming from anthropogenic climate change. Bramble Cay (Maizab Kaur), an ~4ha, low elevation sand cay located in Torres Strait, Australia, supports the only known population of the endangered Bramble Cay melomys Melomys rubicola Thomas, 1924. As a result of a decline in this population noted during previous monitoring to 2004, habitat loss due to erosion of the cay and direct mortality from storm surges were implicated as major threats to this species. This study aimed to confirm the current conservation status of the species, to seek information about the key factor or factors responsible for the population decline and to recover any remaining individuals for a captive insurance population. Methods During three survey periods (December 2011, March 2014 and August–September 2014), a total of 1170 small mammal trap-nights, 60 camera trap-nights, 5h of nocturnal searches and 5h of diurnal searches were undertaken on Bramble Cay. Key results All three survey periods failed to detect any Bramble Cay melomys. The island had experienced a recent, severe reduction in vegetation, which is the primary food resource for the Bramble Cay melomys. Herbaceous cover on the cay decreased from 2.16ha in 2004 to 0.065ha in March 2014 before recovering somewhat to 0.19ha in August–September 2014. Conclusions These results demonstrate that this rodent species has now been extirpated on Bramble Cay. The vegetation decline was probably due to ocean inundation resulting from an increased frequency and intensity of weather events producing extreme high water levels and storm surges, in turn caused by anthropogenic climate change. Implications The loss of the Bramble Cay melomys from Bramble Cay probably represents the first documented mammalian extinction due to human-induced climate change. This event highlights the immediate need to mitigate predicted impacts of sea-level rise and ocean inundation on other vulnerable species occurring on low lying islands and in susceptible coastal zones through captive breeding and reintroduction or other targeted measures.
Social perception of intimate partner violence according to the motivations and sex of the aggressor and the ideology and sex of the observers / Percepción social de la violencia de pareja en función de las motivaciones y sexo del/a agresor/a y de la ideología y sexo de los/as observadores/as
Authors: Zapata-Calvente Antonella-Ludmila , Megías Jesús L.
Published: March 2017

We studied how the sex of the aggressor and their motivations for attacking influence the social perception of intimate partner violence, as well as the sex of the observer and their sexist ideology. University students read a scenario in which both members of a heterosexual couple harmed each other owing to controlling or reactive motivations. After that, they were asked to identify the motivations of each partner and estimate the seriousness of what occurred, the number of aggressions described and the frequency of this kind of episode in real life. The results showed that the men and women properly identified the motivations underlying the aggressive behaviours, considered control violence more serious than reactive violence, and perceived more of the first kind of aggression. However, the men estimated a lower frequency of these episodes in real life, especially episodes of control violence. The ambivalent sexism of the men is related to these assessments. These results are particularly important with regard to the debate on gender symmetry/asymmetry in intimate partner violence.
Characterisation of electric current-treated austenite using misorientation angle distributions in martensite
Authors: Omoigiade Osamudiamen , Haldar Arunansu , Qin Rongshan
Published: March 2017

The angle misorientation distribution of martensite formed from electric current treated and non-treated austenite samples are studied using electron backscatter diffraction. The electric currents are pulsed with a loading width of 80 μs, at a frequency of 100 Hz and current density of 4.21 A/mm2 supplied by a DC Voltage. The majority of angle misorientations are < 5° and exist within the martensite grains, while only a minority of all misorientations are derived from the prior austenite grain boundary and were found to lie in the range 20–50°. Distinct textures develop in both electric current treated and non-treated samples with increased quenching temperature. Analysis of the prior austenite shows reduced grains in the electric current treated samples at all quenching temperatures considered.

This paper is part of a themed issue on Materials in External Fields.
Test of a Nonphysical Barrier Consisting of Light, Sound, and Bubble Screen to Block Upstream Movement of Sea Lampreys in an Experimental Raceway
Authors: Miehls Scott M. , Johnson Nicholas S. , Hrodey Pete J.
Published: March 2017

Control of the invasive Sea Lamprey Petromyzon marinus is critical for management of commercial and recreational fisheries in the Laurentian Great Lakes. Use of physical barriers to block Sea Lampreys from spawning habitat is a major component of the control program. However, the resulting interruption of natural streamflow and blockage of nontarget species present substantial challenges. Development of an effective nonphysical barrier would aid the control of Sea Lampreys by eliminating their access to spawning locations while maintaining natural streamflow. We tested the effect of a nonphysical barrier consisting of strobe lights, low-frequency sound, and a bubble screen on the movement of Sea Lampreys in an experimental raceway designed as a two-choice maze with a single main channel fed by two identical inflow channels (one control and one blocked). Sea Lampreys were more likely to move upstream during trials when the strobe light and low-frequency sound were active compared with control trials and trials using the bubble screen alone. For those Sea Lampreys that did move upstream to the confluence of inflow channels, no combination of stimuli or any individual stimulus significantly influenced the likelihood that Sea Lampreys would enter the blocked inflow channel, enter the control channel, or return downstream.

Received October 4, 2016; accepted March 15, 2017 Published online May 4, 2017
Differences in Stocking Success among Geographically Distinct Stocks of Juvenile Muskellunge in Illinois Lakes
Authors: Diana Matthew J. , Wagner Curtis P. , Wahl David H.
Published: March 2017

Muskellunge Esox masquinongy are broadly distributed across the northern United States and southern Canada. Intraspecific genetic variation suggests the existence of divergent stocks related to residence in major river drainages. Populations and stocks have likely adapted to specific environmental conditions associated with geographic location, especially latitude and the associated thermal regime. In this study, we examined differences in survival and growth among stocks of juvenile Muskellunge stocked into lakes throughout Illinois. Muskellunge from the Ohio River drainage stock, the upper Mississippi River drainage stock, and the current mixed Illinois broodstock were used for comparisons. Stocking mortality was related to temperature and was greatest for Illinois and Ohio River drainage fish that were stocked during the early fall. Mississippi River drainage fish experienced high mortality over the first summer after stocking, resulting in the lowest abundance during the second fall poststocking. In addition to low catch rates, Muskellunge from the Mississippi River drainage were significantly smaller than fish from the Illinois and Ohio River drainage stocks by the second fall. Populations from similar latitudes and climate (Illinois and Ohio) performed the best in terms of survival and growth and should be utilized in future stockings.

Received October 7, 2016; accepted March 15, 2017 Published online May 4, 2017
Urea enhances cell lysis of Schizosaccharomyces pombe ura4 mutants
Authors: Nishino Kohei , Kushima Misaki , Kaino Tomohiro , Matsuo Yasuhiro , Kawamukai Makoto
Published: March 2017

Cell lysis is induced in Schizosaccharomyces pombe ∆ura4 cells grown in YPD medium, which contains yeast extract, polypeptone, and glucose. To identify the medium components that induce cell lysis, we first tested various kinds of yeast extracts from different suppliers. Cell lysis of ∆ura4 cells on YE medium was observed when yeast extracts from OXOID, BD, Oriental, and Difco were used, but not when using yeast extract from Kyokuto. To determine which compounds induced cell lysis, we subjected yeast extract and polypeptone to GC-MS analysis. Ten kinds of compounds were detected in OXOID and BD yeast extracts, but not in Kyokuto yeast extract. Among them was urea, which was also present in polypeptone, and it clearly induced cell lysis. Deletion of the ure2 gene, which is responsible for utilizing urea, abolished the lytic effect of urea. The effect of urea was suppressed by deletion of pub1, and a similar phenotype was observed in the presence of polypeptone. Thus, urea is an inducer of cell lysis in S. pombe ∆ura4 cells.
Brazing method to join a novel Cu54Ni6Zr22Ti18 bulk metallic glass to carbon steel
Authors: Kim Jonghyun , Lee Taekyung
Published: March 2017

This study joined a novel Cu-based bulk metallic glass (BMG) to carbon steel using a brazing process. Cu54Ni6Zr22Ti18 BMG was brazed to SS400 carbon steel using filler metal at 713 K under a compressive stress of 15 MPa for 3 min. Considering the relatively low glass-forming ability, pure Zn and Zn–Ag–Al filler metals were selected to suppress the crystallisation during a reheating thermal cycle. A sound bonding interface without notable chemical diffusion was obtained using the suggested brazing method, particularly with the Zn–Ag–Al filler. This gave rise to considerable improvement in shear bonding strength, from 9 to 45 MPa, when replacing the Zn filler with the Zn–Ag–Al filler. The present method also induced no marked change in phase composition of the BMG due to the low bonding temperature and short bonding time. Slight variations in glass transition temperature and crystallisation temperature would result from a thermal annealing effect.
Dynamic states of swimming bacteria in a nematic liquid crystal cell with homeotropic alignment
Authors: Zhou Shuang , Tovkach Oleh , Golovaty Dmitry , Sokolov Andrey , Aranson Igor S , Lavrentovich Oleg D
Published: March 2017

Flagellated bacteria such as Escherichia coli and Bacillus subtilis exhibit effective mechanisms for swimming in fluids and exploring the surrounding environment. In isotropic fluids such as water, the bacteria change swimming direction through the run-and-tumble process. Lyotropic chromonic liquid crystals (LCLCs) have been introduced recently as an anisotropic environment in which the direction of preferred orientation, the director, guides the bacterial trajectories. In this work, we describe the behavior of bacteria B. subtilis in a homeotropic LCLC geometry, in which the director is perpendicular to the bounding plates of a shallow cell. We demonstrate that the bacteria are capable of overcoming the stabilizing elastic forces of the LCLC and swim perpendicularly to the imposed director (and parallel to the bounding plates). The effect is explained by a finite surface anchoring of the director at the bacterial body; the role of surface anchoring is analyzed by numerical simulations of a rod realigning in an otherwise uniform director field. Shear flows produced by a swimming bacterium cause director distortions around its body, as evidenced both by experiments and numerical simulations. These distortions contribute to a repulsive force that keeps the swimming bacterium at a distance of a few micrometers away from the bounding plates. The homeotropic alignment of the director imposes two different scenarios of bacterial tumbling: one with an 180° reversal of the horizontal velocity and the other with the realignment of the bacterium by two consecutive 90° turns. In the second case, the angle between the bacterial body and the imposed director changes from 90° to 0° and then back to 90°; the new direction of swimming does not correlate with the previous swimming direction.
Circadian Rhythms: A Very Short Introduction
Authors: Foster Russell , Kreitzman Leon
Published: March 2017

The Earth’s daily rotation affects almost every living creature. From dawn through to dusk, there are changes in light, temperature, humidity, and rainfall. However, these changes are regular, rhythmic, and therefore predictable. Thus, the near 24-hour circadian rhythm is innate: a genetically programmed clock. Circadian Rhythms: A Very Short Introduction explains how organisms can ‘know’ the time and reveals what we now understand of the nature and operation of chronobiological processes. Covering variables such as light, the metabolism, human health, and the seasons, it illustrates how jet lag and shift work can impact on human well-being, and considers circadian rhythms alongside a wide range of disorders, from schizophrenia to obesity.
The Future: A Very Short Introduction
Authors: Gidley Jennifer M.
Published: March 2017

Humans have always been driven by both a fear of the unknown and a curiosity to know. They have prophesied, foretold, predicted, and tried to control the future. The Future: A Very Short Introduction considers some of our most burning questions: What is ‘the future’? Is there only one future or are there many possible futures? It introduces the exciting field of future studies, spanning social, cultural, and environmental innovations, as well as technological advances. It asks if the future can ever be truly predicted or if we create our own futures by our thoughts, feelings, and actions. The book concludes by exploring the grand global futures challenges.
The Dead Sea Scrolls: A Very Short Introduction
Authors: Lim Timothy H.
Published: March 2017

The Dead Sea Scrolls: A Very Short introduction discusses the cultural significance of the discovery of the Dead Sea Scrolls and the religious, political, and legal controversies during the seventy years of study since they were found. It looks at the contribution the scrolls have made to our understanding of the Old Testament or Hebrew Bible, and the origins of early Christianity. Exploring the most recent scholarly discussions on the archaeology of Khirbet Qumran, and the study of the biblical texts, the canon, and the history of the Second Temple Period, it considers what the scrolls reveal about the communities closely associated with the scrolls and sectarianism in early Judaism.
The Habsburg Empire: A Very Short Introduction
Authors: Rady Martyn
Published: March 2017

From the 13th to the 20th centuries, Habsburgs ruled much of Central Europe, and for two centuries were rulers of Spain. Through Spain, they acquired lands around the Mediterranean and part of the New World, spreading eastwards to include the Philippines. Reaching from South-East Asia to what is now Ukraine, the Habsburg Empire was truly global. The Habsburg Empire: A Very Short Introduction looks at the history of the Habsburgs from their 10th-century origins in Switzerland, to the dissolution of the Habsburg Empire in 1918. It introduces the pantheon of Habsburg rulers and discusses the lands and kingdoms that made up the Empire and the moments that shaped their history.
Testing Comparability Between Retrospective Life History Data and Prospective Birth Cohort Study Data
Authors: Jivraj Stephen , Goodman Alissa , Ploubidis George B , de Oliveira Cesar
Published: March 2017

Objectives

To determine whether comparable prospective and retrospective data present the same association between childhood and life course exposures and mid-life wellbeing.

Method

Prospective data is taken from the 1958 UK National Child Development Study at age 50 in 2008 and earlier sweeps (n = 8,033). Retrospective data is taken from the English Longitudinal Study of Ageing at ages 50–55 from a life history interview in 2007 (n = 921).

Results

There is a high degree of similarity in the direction of association between childhood exposures that have been prospectively collected in National Child Development Study and retrospectively collected in English Longitudinal Study of Ageing and wellbeing outcomes in mid-life. However, the magnitude of these associations is attenuated substantially by the inclusion of measurements, which are difficult or impossible to capture retrospectively, and are only available in prospective data, such as childhood poverty, cognitive ability, and indices of social and emotional adjustment.

Discussion

The findings on the one hand provide some reassurance to the growing literature using life history data to determine life course associations with later life wellbeing. On the other hand, the findings show an overestimation in the retrospective data, in part, arising from the absence in life history data of childhood measures that are not well suited to retrospective collection.
Variation and Correlation of Protein Molecular Weight Distribution and Semolina Quality Parameters for Durum Genotypes Grown in North Dakota
Authors: Ohm Jae‐Bom , Manthey Frank , Elias Elias M.
Published: March 2017

This research assessed variation of protein molecular weight distribution (MWD) parameters and their correlations with quality characteristics of semolina samples that were obtained from durum genotypes grown in North Dakota. Sodium dodecyl sulfate buffer extractable and unextractable proteins in semolina were analyzed for MWD by size‐exclusion HPLC with a microbore column. ANOVA indicated that quantitative variations of all the HPLC protein fractions were significantly (P < 0.001) influenced by growing environments. The extractable and unextractable gluten proteins correlated differently with semolina gluten characteristics. Both gluten index and mixograph classification showed positive correlations (P < 0.05) with unextractable polymeric proteins and negative correlations (P < 0.05) with extractable gliadins and polymeric proteins. Quantitative variations of gluten proteins greatly influenced spaghetti cooking characteristics. Specifically, cooked spaghetti firmness (CSF) had high and positive simple linear correlations (P < 0.001) with quantity of gluten proteins in both extractable and unextractable fractions. However, a qualitative MWD parameter, percentage of the extractable gliadins in total protein, had a negative genotypic correlation with CSF (r = –0.81, P < 0.01), whereas percentage of the unextractable polymeric proteins had a positive genotypic correlation (r = 0.75, P < 0.01). Those two MWD parameters also showed significant (P < 0.05) variations for genotypes, indicating that they might be useful for screening durum genotypes for pasta cooking quality.
Interrelationships of Flour, Dough, and Bread Properties Under Reduced Salt Level Conditions
Authors: Yovchev Aleksandar , Briggs Connie E. , Stone Andrea K. , Scanlon Martin G. , Tyler Robert T. , Hucl Pierre J. , Nickerson Michael T.
Published: March 2017

The interrelationships between flour quality and the variability in the dough physical properties and bread loaf characteristics were investigated under reduced salt conditions using partial least squares (PLS) regression analysis. Seventy‐two percent of the variability in dough physical properties was explained by the flour quality using a three‐factor PLS model. Damaged starch content (DS), protein content, and farinograph dough development time (DDT) explained the variability of dough creep‐recovery behavior along PLS‐1. Farinograph absorption (FAB), located along PLS‐2, was strongly related to dough adhesiveness, in which adhesiveness was highly correlated to dough stickiness (r = 0.91). Eighty‐nine percent of the variability in bread loaf characteristics was explained by the flour quality using a four‐factor PLS model; the first two PLS factors explained 66% of the variability. The loaf volume was related to a high number of loaf cells, whose expansion resulted in a greater loaf height. The relation between loaf volume and loaf height was expressed more in PLS‐3 than PLS‐1 and PLS‐2. Mean cell wall thickness and mean cell diameter were closely related negatively along PLS‐1, for which DS and farinograph dough stability explained much of the variability in these loaf characteristics. Along the third PLS factor, FAB explained the variability in loaf weight.
Resistance to the SDHI Fungicides Boscalid, Fluopyram, Fluxapyroxad, and Penthiopyrad in Botrytis cinerea from Commercial Strawberry Fields in Spain
Authors: Fernández-Ortuño Dolores , Pérez-García Alejandro , Chamorro Manuel , de la Peña Eduardo , de Vicente Antonio , Torés Juan Antonio
Published: March 2017

Gray mold, caused by the necrotrophic fungus Botrytis cinerea., is one of the most economically important diseases of strawberry. Gray mold control involves the application of fungicides throughout the strawberry growing season; however, B. cinerea isolates resistant to multiple classes of site-specific fungicides have been recently reported in the Spanish gray mold population. Succinate dehydrogenase inhibitors (SDHI) constitute a relatively novel class of fungicides registered for gray mold control representing new alternatives for strawberry growers. In the present study, 37 B. cinerea isolates previously characterized for their sensitivity to boscalid and amino acid changes in the SdhB protein were used to determine the effective concentration that reduces mycelial growth by 50% (EC50) to fluopyram, fluxapyroxad, and penthiopyrad. The present study was also conducted to obtain discriminatory doses to monitor SDHI fungicide resistance in 580 B. cinerea isolates collected from 27 commercial fields in Spain during 2014, 2015, and 2016. The EC50 values ranged from 0.01 to >100 μg/ml for fluopyram, <0.01 to 4.19 μg/ml for fluxapyroxad, and, finally, <0.01 to 59.65 μg/ml for penthiopyrad. Based on these results, as well as findings from a previous publication, the discriminatory doses chosen to examine sensitivities to boscalid, fluopyram, fluxapyroxad, and penthiopyrad were 100, 15, 1, and 6 μg/ml, respectively. Over the course of the 3-year monitoring period, the overall frequencies of resistance to the four SDHI were 56.9, 6.9, 12.9, and 24.6%, respectively. The frequency of boscalid-resistant isolates decreased from 73 to 41% over the years; however, the fluopyram-resistant isolates increased from 5 to 10% after 1 year of registration. Four SDHI resistance patterns were observed in our population, which included patterns I (30%; resistance to boscalid), II (13.8%; resistance to boscalid and penthiopyrad), III (5.7%; boscalid, fluxapyroxad, and penthiopyrad), and IV (7.9%; resistance to boscalid, fluopyram, fluxapyroxad, and penthiopyrad). Patterns I and II were associated with the amino acid substitutions H272R and H272Y; pattern III was associated only with the H272Y mutation; and, finally, pattern IV was associated with the N230I allele in the SdhB subunit. For gray mold management, it is suggested that the simultaneous use of boscalid and penthiopyrad should be limited to one application per season; however, fluxapyroxad and, especially, fluopyram could be used as valid SDHI alternatives for gray mold control, although they should be applied with caution.
Mitochondrial replacement in an iPSC model of Leber’s hereditary optic neuropathy
Authors: Wong Raymond C.B. , Lim Shiang Y. , Hung Sandy S.C. , Jackson Stacey , Khan Shahnaz , Van Bergen Nicole J. , De Smit Elisabeth , Liang Helena H. , Kearns Lisa S , Clarke Linda , Mackey David A. , Hewitt Alex W. , Trounce Ian A. , Pébay Alice
Published: March 2017

Cybrid technology was used to replace Leber hereditary optic neuropathy (LHON) causing mitochondrial DNA (mtDNA) mutations from patient-specific fibroblasts with wildtype mtDNA, and mutation-free induced pluripotent stem cells (iPSCs) were generated subsequently. Retinal ganglion cell (RGC) differentiation demonstrates increased cell death in LHON-RGCs and can be rescued in cybrid corrected RGCs.
Individual heterogeneity and capture-recapture models: what, why and how?
Authors: Gimenez Olivier , Cam Emmanuelle , Gaillard Jean-Michel
Published: March 2017

Variation between and within individuals in life history traits is ubiquitous in natural populations. When affecting fitness-related traits such as survival or reproduction, individual heterogeneity plays a key role in population dynamics and life history evolution. However, it is only recently that properly accounting for individual heterogeneity when studying population dynamics of free-ranging populations has been made possible through the development of appropriate statistical models. We aim here to review case studies of individual heterogeneity in the context of capture-recapture models for the estimation of population size and demographic parameters with imperfect detection. First, we define what individual heterogeneity means and clarify the terminology used in the literature. Second, we review the literature and illustrate why individual heterogeneity is used in capture-recapture studies by focusing on the detection of life-history trade-offs, including senescence. Third, we explain how to model individual heterogeneity in capture-recapture models and provide the code to fit these models (https://github.com/oliviergimenez/indhet_in_CRmodels). The distinction is made between situations in which heterogeneity is actually measured and situations in which part of the heterogeneity remains unobserved. Regarding the latter, we outline recent developments of random-effect models and finite-mixture models. Finally, we discuss several avenues for future research.
Replication defective viral genomes exploit a cellular pro-survival mechanism to establish paramyxovirus persistence
Authors: Xu Jie , Sun Yan , Li Yize , Ruthel Gordon , Weiss Susan R. , Raj Arjun , Beiting Daniel , López Carolina B.
Published: March 2017

Replication defective viral genomes (DVGs) generated during virus replication are the primary triggers of antiviral immunity in many RNA virus infections. However, DVGs can also facilitate viral persistence. Why and how these two opposing functions of DVGs are achieved remain unknown. Here we report that during Sendai and respiratory syncytial virus infections DVGs selectively protect a subpopulation of cells from death and promote the establishment of persistent infections. We find that during Sendai virus infection this phenotype results from DVGs stimulating a MAVS-mediated TNF response that drives apoptosis of highly infected cells while extending the survival of cells enriched in DVGs. The pro-survival effect of TNF depends on the activity of the TNFR2/TRAF1 pathway that is regulated by MAVS signaling. These results identify TNF as a pivotal factor in determining cell fate during a viral infection and delineate a MAVS/TNFR2-mediated mechanism that drives the persistence of otherwise acute viruses.
Genome Wide Association Analyses Based on Broadly Different Specifications for Prior Distributions, Genomic Windows, and Estimation Methods
Authors: Chen Chunyu , Steibel Juan P. , Tempelman Robert J.
Published: March 2017

A popular strategy (EMMAX) for genome wide association (GWA) analysis fits all marker effects as classical random effects (i.e., Gaussian prior) by which association for the specific marker of interest is inferred by treating its effect as fixed. It seems more statistically coherent to specify all markers as sharing the same prior distribution, whether it is Gaussian, heavy-tailed (BayesA), or has variable selection specifications based on a mixture of, say, two Gaussian distributions (SSVS). Furthermore, all such GWA inference should be formally based on posterior probabilities or test statistics as we present here, rather than merely being based on point estimates. We compared these three broad categories of priors within a simulation study to investigate the effects of different degrees of skewness for quantitative trait loci (QTL) effects and numbers of QTL using 43,266 SNP marker genotypes from 922 Duroc-Pietrain F2 cross pigs. Genomic regions were based either on single SNP associations, on non-overlapping windows of various fixed sizes (0.5 to 3 Mb) or on adaptively determined windows that cluster the genome into blocks based on linkage disequilibrium (LD). We found that SSVS and BayesA lead to the best receiver operating curve properties in almost all cases. We also evaluated approximate marginal a posteriori (MAP) approaches to BayesA and SSVS as potential computationally feasible alternatives; however, MAP inferences were not promising, particularly due to their sensitivity to starting values. We determined that it is advantageous to use variable selection specifications based on adaptively constructed genomic window lengths for GWA studies.

Genome wide association (GWA) analyses strategies have been improved by simultaneously fitting all marker effects when inferring upon any single marker effect, with the most popular distributional assumption being normality. Using data generated from 43,266 genotypes on 922 Duroc-Pietrain F2 cross pigs, we demonstrate that GWA studies could particularly benefit from more flexible heavy-tailed or variable selection distributional assumptions. Furthermore, these associations should not just be based on single markers or even genomic windows of markers of fixed physical distances (0.5 − 3.0 Mb) but based on adaptively determined genomic windows using linkage disequilibrium information.
Anatomical and functional organization of the human substantia nigra and its connections
Authors: Zhang Yu , Larcher Kevin , Misic Bratislav , Dagher Alain
Published: March 2017

We investigated the anatomical and functional organization of the human substantia nigra (SN) using diffusion and functional MRI data from the Human Connectome Project. We identified a tripartite connectivity-based parcellation of SN with a limbic, cognitive and motor arrangement. The medial SN connects with limbic striatal and cortical regions and encodes value (greater response to monetary wins than losses during fMRI), while the ventral SN connects with associative regions of cortex and striatum and encodes salience (equal response to wins and losses). The lateral SN connects with somatomotor regions of striatum and cortex and also encodes salience. Connectivity within the value-coding medial SN network was associated with a measure of decisional impulsivity, while the salience-coding ventral SN network was associated with motor impulsivity. In sum, there is anatomical and functional heterogeneity of human SN, and separate SN networks underpin value versus salience coding, and impulsive choice versus impulsive action.
Polygenicity and epistasis underlie fitness-proximal traits in theCaenorhabditis elegansmultiparental experimental evolution (CeMEE) panel
Authors: Noble Luke M. , Chelo Ivo , Guzella Thiago , Afonso Bruno , Riccardi David D. , Ammerman Patrick , Dayarian Adel , Carvalho Sara , Crist Anna , Pino-Querido Ania , Shraiman Boris , Rockman Matthew V. , Teotónio Henrique
Published: March 2017

Understanding the genetic basis of complex traits remains a major challenge in biology. Polygenicity, phenotypic plasticity and epistasis contribute to phenotypic variance in ways that are rarely clear. This uncertainty is problematic for estimating heritability, for predicting individual phenotypes from genomic data, and for parameterizing models of phenotypic evolution. Here we report a recombinant inbred line (RIL) quantitative trait locus (QTL) mapping panel for the hermaphroditic nematodeCaenorhabditis elegans, theC. elegansmultiparental experimental evolution (CeMEE) panel. The CeMEE panel, comprising 507 RILs, was created by hybridization of 16 wild isolates, experimental evolution at moderate population sizes and predominant outcrossing for 140-190 generations, and inbreeding by selfing for 13-16 generations. The panel contains 22% of single nucleotide polymorphisms known to segregate in natural populations, and complements existing mapping resources forC. elegansby providing high nucleotide diversity across >95% of the genome. We apply it to study the genetic basis of two fitness components, fertility and hermaphrodite body size at time of reproduction, with high broad sense heritability in the CeMEE. While simulations show we should detect common alleles with additive effects as small as 5%, at gene-level resolution, the genetic architectures of these traits does not feature such alleles. We instead find that a significant fraction of trait variance, particularly for fertility, can be explained by sign epistasis with weak main effects. In congruence, phenotype prediction, while generally poor (r2< 10%), requires modeling epistasis for optimal accuracy, with most variance attributed to the highly recombinant, rapidly evolving chromosome arms.
Mechanochemical synthesis ofN-salicylideneaniline: thermosalient effect of polymorphic crystals
Authors: Mittapalli Sudhir , Sravanakumar Perumalla D. , Nangia Ashwini
Published: March 2017

Polymorphs of the dichloro derivative ofN-salicylideneaniline exhibit mechanical responses such as jumping (Forms I and III) and exploding (Form II) in its three polymorphs. The molecules are connectedviathe amide N—H...O dimer synthon and C—Cl...O halogen bond in the three crystal structures. A fourth high-temperature Form IV was confirmed by variable-temperature single-crystal X-ray diffraction at 180°C. The behaviour of jumping exhibited by the polymorphic crystals of Forms I and III is due to the layered sheet morphology and the transmission of thermal stress in a single direction, compared with the corrugated sheet structure of Form II such that heat dissipation is more isotropic causing blasting. The role of weak C—Cl...O interactions in the thermal response of molecular crystals is discussed.
Edge-2-transitive trinodal polyhedra and 2-periodic tilings
Authors: Delgado-Friedrichs Olaf , O'Keeffe Michael
Published: March 2017

All trinodal, edge-2-transitive polyhedra and 2-periodic tilings are enumerated and described. These are of special interest for the design and synthesis of materials such as metal–organic polyhedra and frameworks.
Diffuse single-crystal scattering corrected for molecular form factor effects
Authors: Schmidt Ella , Neder Reinhard B.
Published: March 2017

This paper shows that chemical short-range order in two-component molecular crystals can be solved directly by separating the influence of the molecular form factor from the diffraction pattern. This novel technique is demonstrated by analysing the diffuse scattering of tris-tert-butyl-1,3,5-benzene tricarboxamide.
Groupoids and labelled quotient graphs: a topological analysis of the modular structure in pyroxenes
Authors: Eon Jean-Guillaume
Published: March 2017

The analysis of the modular structure of pyroxenes, recently discussed in Nespolo & Aroyo [Eur. J. Mineral.(2016),28, 189–203], has been performed on the respective labelled quotient graphs (LQGs). It is shown that the structure and maximum symmetry of the module,i.e.its layer group, can be determined directly from the LQG. Partial symmetry operations between different modules have been associated with automorphisms of the quotient graph that may not be consistent with net voltages over the respective cycles. These operations have been shown to generate the pyroxene groupoid structure.