bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental evidence of transition between dynamical and kinematical diffraction regimes in ion-implanted Si observed through X-ray multiple-beam diffraction mappings
Authors: Calligaris Guilherme A. , Lang Rossano , Bettini Jefferson , dos Santos Adenilson O. , Cardoso Lisandro P.
Published: October 2016

In this paper, the dependence of a Laue diffraction streak on the crystalline perfection of Xe-implanted Si(001) substrates is presented, based on the observation in the X-ray multiple diffraction (XRMD) mappings, as an experimental evidence of the transition between dynamical and kinematical diffraction regimes. A direct observation of the implanted region by transmission electron microscopy revealed an amorphous Si layer, which recrystallizes into a heavily twinned and faulted microstructure after thermal treatment at 800 °C. Besides the lattice damages, the annealing induces the formation of Xe bubbles. Both singularly affect the XRMD pattern, primarily the four-fold streaks profile of the (000)(002)(11¯1¯)(11¯3) four-beam simultaneous case when compared with the pristine Si pattern, highlighting the intra- and inter-block diffractions and the role played by the primary extinction effect. Such features provide information on the dominant diffraction regime. The findings are also discussed and compared to the conventional reciprocal space mappings via the asymmetric Si(113) reflection.
Asymmetry in structural response of inner and outer transmembrane segments of CorA protein by a coarse-grain model
Authors: Kitjaruwankul Sunan , Khrutto Channarong , Sompornpisut Pornthep , Farmer B. L. , Pandey R. B.
Published: October 2016

Structure of CorA protein and its inner (i.corA) and outer (o.corA) transmembrane (TM) components are investigated as a function of temperature by a coarse-grained Monte Carlo simulation. Thermal response of i.corA is found to differ considerably from that of the outer component, o.corA. Analysis of the radius of gyration reveals that the inner TM component undergoes a continuous transition from a globular conformation to a random coil structure on raising the temperature. In contrast, the outer transmembrane component exhibits an abrupt (nearly discontinuous) thermal response in a narrow range of temperature. Scaling of the structure factor shows a globular structure of i.corA at a low temperature with an effective dimension D ∼ 3 and a random coil at a high temperature with D ∼ 2. The residue distribution in o.corA is slightly sparser than that of i.corA in a narrow thermos-responsive regime. The difference in thermos-response characteristics of these components (i.corA and o.corA) may reflect their unique transmembrane functions.
Perspective: Understanding of ripening growth model for minimum residual PbI2 and its limitation in the planar perovskite solar cells
Authors: Kim Se-Yun , Jo Hyo Jeong , Sung Shi-Joon , Kim Dae-Hwan
Published: October 2016

The power conversion efficiency of lead halide perovskite solar cells recently surpassed 22.1%. In this study, we suggest the perovskite absorber growth mechanism of the two-step process could be explained by an Ostwald ripening growth model for planar-structure perovskite solar cells. We attempt to find out the source of two main problems such as unreacted PbI2 and non-uniformed morphology by the proposed ripening growth mechanism and experimental results. This growth mechanism opens the way toward understanding a key aspect of the photovoltaic operation of high-efficiency, two-step perovskite solar cells.
Oxide stoichiometry-controlled TaOx-based resistive switching behaviors
Authors: Baek Gwang Ho , Lee Ah Rahm , Kim Tae Yoon , Im Hyun Sik , Hong Jin Pyo
Published: October 2016

We examine the influence of variable oxygen concentration in TaOx active layers on the forming process and bipolar resistive switching (BRS) features of TaOx-based resistive switching cells. TaOx active layers prepared using various rf sputtering powers were systematically analyzed to identify the relation between initial compositions and BRS behavior. Proper control of oxygen vacancy concentration was clearly identified as a basic factor in ensuring typical BRS features without affecting the structural properties. We describe the possible origins of both conduction and switching based on the variation of oxygen concentrations initially provided by the growth conditions.
Tunable, high-sensitive measurement of inter-dot transition via tunneling induced absorption
Authors: Peng Yandong , Yang Aihong , Chen Bing , Li Lei , Liu Shande , Guo Hongju
Published: October 2016

A tunable, narrow absorption spectrum induced by resonant tunneling is demonstrated and proposed for measuring interdot tunneling. Tunneling-induced absorption (TIA) arises from constructive interference between different transition paths, and the large nonlinear TIA significantly enhances the total absorption. The narrow nonlinear TIA spectrum is sensitive to inter-dot tunneling, and its sensor characteristics, including sensitivity and bandwidth, are investigated in weak-coupling and strong-coupling regimes, respectively.
Magnetic field dependence of the internal quality factor and noise performance of lumped-element kinetic inductance detectors
Authors: Flanigan D. , Johnson B. R. , Abitbol M. H. , Bryan S. , Cantor R. , Day P. , Jones G. , Mauskopf P. , McCarrick H. , Miller A. , Zmuidzinas J.
Published: October 2016

We present a technique for increasing the internal quality factor of kinetic inductance detectors (KIDs) by nulling ambient magnetic fields with a properly applied magnetic field. The KIDs used in this study are made from thin-film aluminum, they are mounted inside a light-tight package made from bulk aluminum, and they are operated near 150 mK. Since the thin-film aluminum has a slightly elevated critical temperature (Tc = 1.4 K), it therefore transitions before the package (Tc = 1.2 K), which also serves as a magnetic shield. On cooldown, ambient magnetic fields as small as approximately 30 µT can produce vortices in the thin-film aluminum as it transitions because the bulk aluminum package has not yet transitioned and therefore is not yet shielding. These vortices become trapped inside the aluminum package below 1.2 K and ultimately produce low internal quality factors in the thin-film superconducting resonators. We show that by controlling the strength of the magnetic field present when the thin film transitions, we can control the internal quality factor of the resonators. We also compare the noise performance with and without vortices present, and find no evidence for excess noise beyond the increase in amplifier noise, which is expected with increasing loss.
Two-dimensional hydrodynamic flow focusing in a microfluidic platform featuring a monolithic integrated glass micronozzle
Authors: Liu Yifan , Shen Yusheng , Duan Lian , Yobas Levent
Published: October 2016

Two-dimensional hydrodynamic flow focusing is demonstrated through a microfluidic device featuring a monolithic integrated glass micronozzle inside a flow-focusing geometry. Such a coaxial configuration allows simple one-step focusing of a sample fluid stream, jetted from the micronozzle tip, in both in-plane and out-of-plane directions. The width of the focused filament can be precisely controlled and further scaled down to the submicrometer regime to facilitate rapid hydrodynamic mixing. Fluorescence quenching experiments reveal ultra-fast microsecond mixing of the denaturant into the focused filament. This device offers new possibilities to a set of applications such as the study of protein folding kinetics.
Fabrication of normally-off GaN nanowire gate-all-around FET with top-down approach
Authors: Im Ki-Sik , Won Chul-Ho , Vodapally Sindhuri , Caulmilone Raphaël , Cristoloveanu Sorin , Kim Yong-Tae , Lee Jung-Hee
Published: October 2016

Lateral GaN nanowire gate-all-around transistor has been fabricated with top-down process and characterized. A triangle-shaped GaN nanowire with 56 nm width was implemented on the GaN-on-insulator (GaNOI) wafer by utilizing (i) buried oxide as sacrificial layer and (ii) anisotropic lateral wet etching of GaN in tetramethylammonium hydroxide solution. During subsequent GaN and AlGaN epitaxy of source/drain planar regions, no growth occurred on the nanowire, due to self-limiting growth property. Transmission electron microscopy and energy-dispersive X-ray spectroscopy elemental mapping reveal that the GaN nanowire consists of only Ga and N atoms. The transistor exhibits normally-off operation with the threshold voltage of 3.5 V and promising performance: the maximum drain current of 0.11 mA, the maximum transconductance of 0.04 mS, the record off-state leakage current of ∼10−13 A/mm, and a very high Ion/Ioff ratio of 108. The proposed top-down device concept using the GaNOI wafer enables the fabrication of multiple parallel nanowires with positive threshold voltage and is advantageous compared with the bottom-up approach.
Formation energies of intrinsic point defects in monoclinic VO2 studied by first-principles calculations
Authors: Cui Yuanyuan , Liu Bin , Chen Lanli , Luo Hongjie , Gao Yanfeng
Published: October 2016

VO2 is an attractive candidate for intelligent windows and thermal sensors. There are challenges for developing VO2-based devices, since the properties of monoclinic VO2 are very sensitive to its intrinsic point defects. In this work, the formation energies of the intrinsic point defects in monoclinic VO2 were studied through the first-principles calculations. Vacancies, interstitials, as well as antisites at various charge states were taken into consideration, and the finite-size supercell correction scheme was adopted as the charge correction scheme. Our calculation results show that the oxygen interstitial and oxygen vacancy are the most abundant intrinsic defects in the oxygen rich and oxygen deficient condition, respectively, indicating a consistency with the experimental results. The calculation results suggest that the oxygen interstitial or oxygen vacancy is correlated with the charge localization, which can introduce holes or electrons as free carriers and subsequently narrow the band gap of monoclinic VO2. These calculations and interpretations concerning the intrinsic point defects would be helpful for developing VO2-based devices through defect modifications.
The occurrence and relative abundance of small terrestrial mammals on Theda Station in the Northern Kimberley, Western Australia
Authors: Olds Liberty G. M. , Myers Cecilia , Cook Henry , Schembri Brendan , Jackson Christopher , Evans Nick , Charles Brian , Waina Rowan , Breed William G. , Taggart David A.
Published: October 2016

Significant gaps in knowledge currently exist regarding the small mammal fauna of the Northern Kimberley (NOK) bioregion. Theda Station is a previously unsurveyed pastoral lease in the NOK. The aim of the current study was to determine the presence of small mammals (non-volant, <2 kg) on Theda Station and to compare these findings with those recently obtained on the adjacent Doongan Station. Between 2006 and 2014, 226 site surveys were conducted across 69 sites, with over 26 000 trap-nights encompassing a range of habitats. Thirteen of the 27 small mammal species known to occur in the NOK were detected. Four species (Pseudomys nanus, Rattus tunneyi, Zyzomys argurus and Sminthopsis virginiae) were common, five (Pseudomys delicatulus, Pseudantechinus ningbing, Dasyurus hallucatus, Isoodon macrourus and Petropseudes dahli) were detected less frequently, and four (Leggadina lakedownensis, Hydromys chrysogaster, Planigale maculata and Petaurus breviceps) were occasionally recorded. Our study provides important baseline data for small mammals in this region. It highlights the lack of detailed knowledge of both the presence of, and temporal fluctuations in, the region’s small mammal fauna. This study supports a non-uniform distribution of the small mammal fauna across the NOK, with Theda Station lying within a transition zone between the high rainfall rugged coastal and near-coastal areas and the lower rainfall areas of the east.
Travel and tuberculosis
Authors: Coulter Christopher
Published: October 2016

Australians frequently travel to countries with a high incidence of tuberculosis (TB). What risk does TB pose to travellers and what can be done to mitigate this risk?
Bidirectional cross-linguistic relations of first and second language skills in reading comprehension of Spanish-speaking English learners
Authors: Gottardo Alexandra , Javier Christine , Farnia Fataneh , Mak Lorinda , Geva Esther
Published: October 2016

This study examines the bidirectional, cross-linguistic associations between language and word-level reading skills and reading comprehension for 51 students in grades 4 to 6 who speak Spanish as first language (L1) and English as second language (L2). Within-language predictors of reading comprehension were consistent with the simple view of reading. We found unidirectional cross-linguistic associations between Spanish word reading and English reading comprehension. However, the results do not support a cross-linguistic association between English word reading and Spanish reading comprehension. Specifically, results indicate that although L1 and L2 language and reading constructs correlate, L2 skills do not strongly contribute to L1 reading comprehension. Findings are discussed in terms of possible factors that might influence potential cross-language relations among Spanish and English measures.
The role of L1 and L2 reading on L1 preservation and positive cross-linguistic transfer among sequential bilinguals
Authors: Zaretsky Elena
Published: October 2016

Previous research shows strong evidence of positive cross-linguistic transfer as a factor of L1 literacy. Moreover, research shows that L1 literacy supports the preservation of L1 language skills while learning L2, as oral and written languages are highly interdependent. Two theoretical frameworks can be instrumental in accounting for cross-linguistic transfer: The constructive analysis hypothesis suggests that the closer L1 and L2 are typologically, the more cross-linguistic transfer should be observed. The interdependence hypothesis postulates that bilingual transfer is also supported by L1 proficiency. These hypotheses were tested in oral language experiment, comparing typologically different languages (L1 Russian and L2 English) with different orthographic depth and language-specific characteristics. The study examines the use of morphosyntactic and lexical structures through story retelling in L1 and L2 by 13 Russian-English bilingual children (Mage = 8;2) who were readers in their L1 as well as in their L2. The results indicate a strong effect of L1 reading skills on children’s ability to use appropriate lexical and syntactic processes in their L1 and L2 narratives as well as on the reduction of L1 grammatical errors, one of the most sensitive aspects of Russian inflectional morphology. These results support the interdependence hypothesis of cross-linguistic transfer.
Towards a theory of pronominal verb constructions in Spanish
Authors: Armstrong Grant
Published: October 2016

This paper proposes a unified account of three types of constructions in which the se clitic appears, which are dubbed pronominal verb constructions (PVCs) . unaccusatives like acatarrar-se (get sick), unergatives like quejar-se (complain) and transitives like zampar-se algo (to wolf something down). The main claims are (i) that the verbs in question represent classes that are specified to select a “defective” head (= a head that does not introduce a theta role and/or assign case) in their predicate-argument argument structure and (ii) Spanish marks such defective heads as [ϕ], a diacritic that triggers insertion of se post-syntactically at T. The different classes of PVCs are derived from the type of defective head that is selected, Voice[ϕ] in the case of intransitives and P[ϕ] in the case of transitives.
On the grammaticality of recomplementation in Spanish
Authors: Frank Joshua
Published: October 2016

In English, an overt secondary complementizer has been described as a grammatical violation, a claim that cannot be corroborated for Spanish. The present study fills this gap in the literature by asking whether the overt variety is associated with a decrement in acceptability judgment when compared to the null variety. Results from a speeded aural acceptability judgment task suggest that there is indeed a significant decrement in acceptability rating. This finding is robust across both statement and question constructions. A processing-based account is offered in order to unify results from both Spanish and English. Importantly, given that the native Spanish speakers do not fully reject the overt variety, the proposed account is meant to complement rather than to replace existing grammar-based accounts.
Synchronic change in a multidialectal Spanish community
Authors: Domínguez Laura , Hicks Glyn
Published: October 2016

Recent developments in linguistic theory have successfully reconciled diachronic syntactic change (Biberauer & Roberts, 2006; Breibarth, Lucas, & Willis, 2008; Roberts, 2007) and intra-speaker variation (Adger & Smith, 2005, 2010; Henry, 1995; Barbiers, 2005) with Minimalist models of the language faculty. Cases of L1 attrition, however, whereby morphosyntactic properties in stable adult grammars undergo change, remain unaccounted for by Minimalist theory. Using evidence from the realisation of null and postverbal subjects in the grammar of two groups of native Spanish speakers in different bilingual settings, (Miami and the U.K.) we demonstrate that L1 attrition in language contact situations can similarly be accommodated within Minimalist theory, driven by changes to the lexical feature specifications of functional categories (Adger & Smith, 2010; Gallego, 2011; Holmberg, 2010).
Generalized gradability and extremeness in Puerto Rican Spanish
Authors: Padilla-Reyes Ramón , Gutiérrez-Rexach Javier , González-Rivera Melvin
Published: October 2016

The expression of extremeness in Puerto Rican Spanish is encoded in a series of modifiers, which are attached to adjectival, nominal or verbal elements. The proper treatment of this phenomenon requires a generalization of gradability and modification transcategorially. A semantic account is presented in which extremeness is mapped along several contextually-dependent dimensions, which are sensitive to the properties of the event associated to the expression in the scope of the modifier.
On the simplification of a prosodic inventory
Authors: Sessarego Sandro , Rao Rajiv
Published: October 2016

This paper analyzes the declarative intonation of Afro-Bolivian Spanish (ABS) in terms of the realization of pitch accents and phrase boundary tones. We observe that the inventory of these phonological targets in ABS is much more reduced than what has been encountered in other native varieties of Spanish. Our ABS speakers show evidence of duplicating nuclear and prenuclear pitch accents, as well as boundary configurations, at both levels of phrasing. The results suggest that certain aspects of ABS intonation may be considered the result of conventionalized advanced second language acquisition processes (Sessarego, 2013a) stemming from an incomplete mastery of the phonology/pragmatics interface.
The prosody-pragmatics interface in the pragmaticalization of ¡Hombre! as a discourse marker
Authors: Regan Brendan
Published: October 2016

The current study, using a mixed methods approach of qualitative discourse analysis and quantitative phonetic analysis based on the framework of interactional prosody (Couper-Kuhlen, 2001; Couper-Kuhlen & Selting, 1996; Selting, 2010), analyzes the pragmaticalized multifunctional discourse marker hombre ‘man’ in Andalusian Spanish. Discourse analyses of 28 sociolinguistic interviews reveals three major discourse functions of hombre. Phonological and phonetic analyses reveal that prosodic cues vary per category, demonstrating that prosody serves as a co-occurring contextualization cue (Gumperz, 1982; Tannen, 1993) in addition to lexical and syntactic cues to signal intended meaning. The study aims to unite discourse and phonetic analysis through interactional prosody in the subfield of variational pragmatics in order to holistically investigate pragmaticalized multifunctional discourse markers.
An analysis of subjunctive frequency and semantic predictors of mood in Central Argentinian Spanish
Authors: Gallego Muriel
Published: October 2016

This study reports on distinct patterns of mood alternation among monolingual speakers of Spanish in central Argentina. A total of 224 participants completed two written tasks online. In the mood selection preference task, subjunctive licensing was analyzed in terms of semantic predictors of volition, recommendation, comment and uncertainty. In the guided writing task, subjunctive use in semi-spontaneous production was measured. Female older speakers produced subjunctive at higher rates, whereas it was almost non-existent among younger males. As for semantic predictors, subjunctive was categorically preferred by older speakers and indicative acceptance was observed among younger generations. While volitional and directives operated as robust subjunctive predictors across groups, indicative was preferred for comment and uncertainty, mainly among younger speakers.
Double possession in Peruvian Amazonian Spanish
Authors: Rodríguez-Mondonedo Miguel , Fafulas Stephen
Published: October 2016

In this study we analyze the phenomenon known as “double possession” in monolingual and bilingual Spanish communities located in the Peruvian Amazon. Our data come from sociolinguistic interviews conducted with bilingual Bora-Spanish speakers and monolingual Iquitos Spanish speakers. From a syntactic view, we claim that double possessor constructions in Peruvian Amazonian Spanish arise from small-n incorporation into D, rendering the possessive determiner. We explore the extent to which this movement is motivated by language contact, potentially triggering the remnants of an Old Spanish doubling structure, or an innovation due to the specific contact situation of these communities. Our investigation contributes to theoretical discussions of micro-parametric variation and documents semi-spontaneous speech from a less commonly examined region of the Spanish-speaking world.
Chapter 1. Enregistering the North
Authors: Beal Joan C.
Published: October 2016

William Bullein’s Dialogue Against the Fever Pestilence (1st ed. 1564) was
reprinted by the Early English Text Society in 1888 and later included in Early
English Books Online (EEBO). Although much of the scholarly interest in the text
has been in the areas of medical history (e.g. Mitchell 1959) and Early Modern
English literature (e.g. Griffiths 2007), it has recently caught the attention of
scholars interested in dialects of Early Modern English (Taavitsainen,
Melchers and Pahti (eds.) 1999; Wales 2006; Ruano Garcia 2010). However, the
history of Bullein’s Dialogue as a source of dialect material goes back to the
time of the EETS reprint: it was included in R. O. Heslop’s (1896) bibliographical
list of works illustrative of the dialect of Northumberland and Heslop used
it as a source for some of the entries in his Northumberland Words (1892–4).
Since Heslop’s glossary has, in its turn been widely cited as an authoritative
source for information on traditional Northumbrian dialects, the influence of
Bullein’s Dialogue has been considerable. In this paper, I discuss Bullein’s use of
Northumbrian dialect within the framework of indexicality and enregisterment
(Agha 2003). I argue that Bullein, who had had contact with speakers of
Northumbrian dialect whilst practising as a physician in Tynemouth, chose to
portray the character of Mendicus by referencing features that already indexed
Northern stereotypes due to their association with the Border Ballads. In doing
this, Bullein both drew on and contributed to the enregisterment of Northern,
and, more specifically, Northumbrian dialect as ‘outlandish'.
Chapter 5. Decoding the parentheses in Shakespeare’s Coriolanus
Authors: Chen Guohua , Duan Suping
Published: October 2016

Though it has been pointed out that Shakespeare uses the figure parenthesis
“extensively, especially in his later plays” (Joseph 1947: 57), it has
been more often marginalized, if not totally neglected. The present paper
contends that parenthesis contributes greatly to characterization and the
development of conflicts in dramatic texts. Through a detailed analysis
of its use in Shakespeare’s Coriolanus, this paper attempts to illustrate the significance of
parenthesis. At the rhetorical level, parenthesis may have the dual functions of
varying and amplifying as differentiated by Adamson (1999). For example, a
parenthesis may take the form of a noun phrase in apposition to its antecedent
as a way of varying and it may take the form of a non-restrictive relative clause
as a way of amplifying, and therefore helps achieve diverse rhetorical effects
and convey rich rhetorical meanings. For this reason, a functional study of the
subjective and interpersonal function of parentheses can provide clues to a deeper understanding
of speaker-hearer relationship, hence of overall dramatic characterization
and conflict management.
Chapter 9. Dismantling narrative modes
Authors: Sotirova Violeta
Published: October 2016

This study examines Virginia Woolf ’s authorial revisions of the opening of Mrs
Dalloway and their implications for narrative theory. I compare passages from
the short story ‘Mrs Dalloway in Bond Street’ and the early drafts of ‘The Hours’
with the published novel and show that there is a consistent pattern of revision
which complicates the representation of character consciousness. This complexity
lies in the dismantling of narrative modes used for the representation of
consciousness, most typically by conflating them into the syntactic boundaries
of a single sentence. From a stylistic standpoint, the dissolution of the syntactic
boundaries between narrative modes challenges most standard accounts of
speech and thought presentation which posit narrative modes as discrete syntactic
units. From a narratological standpoint, this syntactic and semantic dismantling
of narrative modes reflects an attempt at representing distinct facets of
consciousness as simultaneous phenomena of experience. Thus, Woolf ’s revised
text captures the simultaneity of, for instance, a character’s less conscious perception
of the narrative world and the more consciously executed reflective thought,
or of a character’s internal state and direct speech, grafting them into the text as
narrative modes that are syntactically and semantically interdependent.
Genome shuffling of Lactobacillus plantarum C88 improves adhesion
Authors: Zhao Yujuan , Duan Cuicui , Gao Lei , Yu Xue , Niu Chunhua , Li Shengyu
Published: October 2016

Genome shuffling is an important method for rapid improvement in microbial strains for desired phenotypes. In this study, ultraviolet irradiation and nitrosoguanidine were used as mutagens to enhance the adhesion of the wild-type Lactobacillus plantarum C88. Four strains with better property were screened after mutagenesis to develop a library of parent strains for three rounds of genome shuffling. Fusants F3-1, F3-2, F3-3, and F3-4 were screened as the improved strains. The in vivo and in vitro tests results indicated that the population after three rounds of genome shuffling exhibited improved adhesive property. Random Amplified Polymorphic DNA results showed significant differences between the parent strain and recombinant strains at DNA level. These results suggest that the adhesive property of L. plantarum C88 can be significantly improved by genome shuffling. Improvement in the adhesive property of bacterial cells by genome shuffling enhances the colonization of probiotic strains which further benefits to exist probiotic function.
The Ska complex promotes Aurora B activity to ensure chromosome biorientation
Authors: Redli Patrick M. , Gasic Ivana , Meraldi Patrick , Nigg Erich A. , Santamaria Anna
Published: October 2016

Chromosome biorientation and accurate segregation rely on the plasticity of kinetochore–microtubule (KT-MT) attachments. Aurora B facilitates KT-MT dynamics by phosphorylating kinetochore proteins that are critical for KT-MT interactions. Among the substrates whose microtubule and kinetochore binding is curtailed by Aurora B is the spindle and kinetochore-associated (Ska) complex, a key factor for KT-MT stability. Here, we show that Ska is not only a substrate of Aurora B, but is also required for Aurora B activity. Ska-deficient cells fail to biorient and display chromosome segregation errors underlying suppressed KT-MT turnover. These defects coincide with KNL1–Mis12–Ndc80 network hypophosphorylation, reduced mitotic centromere-associated kinesin localization, and Aurora B T-loop phosphorylation at kinetochores. We further show that Ska requires its microtubule-binding capability to promote Aurora B activity in cells and stimulates Aurora B catalytic activity in vitro. Finally, we show that protein phosphatase 1 counteracts Aurora B activity to enable Ska kinetochore accumulation once biorientation is achieved. We propose that Ska promotes Aurora B activity to limit its own microtubule and kinetochore association and to ensure that KT-MT dynamics and stability fall within an optimal balance for biorientation.
Trade-offs in marine protection: multispecies interactions within a community-led temperate marine reserve
Authors: Howarth Leigh M. , Dubois Pascal , Gratton Paul , Judge Matthew , Christie Brian , Waggitt James J. , Hawkins Julie P. , Roberts Callum M. , Stewart Bryce D.
Published: October 2016

This study investigated the effects of a community-led temperate marine reserve in Lamlash Bay, Firth of Clyde, Scotland, on commercially important populations of European lobster (Homarus gammarus), brown crab (Cancer pagurus), and velvet swimming crabs (Necora puber). Potting surveys conducted over 4 years revealed significantly higher catch per unit effort (cpue 109% greater), weight per unit effort (wpue 189% greater), and carapace length (10–15 mm greater) in lobsters within the reserve compared with control sites. However, likely due to low levels of recruitment and increased fishing effort outside the reserve, lobster catches decreased in all areas during the final 2 years. Nevertheless, catch rates remained higher within the reserve across all years, suggesting the reserve buffered these wider declines. Additionally, lobster cpue and wpue declined with increasing distance from the boundaries of the marine reserve, a trend which tag–recapture data suggested were due to spillover. Catches of berried lobster were also twice as high within the reserve than outside, and the mean potential reproductive output per female was 22.1% greater. It was originally thought that higher densities of lobster within the reserve might lead to greater levels of aggression and physical damage. However, damage levels were solely related to body size, as large lobsters >110 mm had sustained over 218% more damage than smaller individuals. Interestingly, catches of adult lobsters were inversely correlated with those of juvenile lobsters, brown crabs, and velvet crabs, which may be evidence of competitive displacement and/or predation. Our findings provide evidence that temperate marine reserves can deliver fisheries and conservation benefits, and highlight the importance of investigating multispecies interactions, as the recovery of some species can have knock-on effects on others.
TTG and Potassic Granitoids in the Eastern North China Craton: Making Neoarchean Upper Continental Crust during Micro-continental Collision and Post-collisional Extension
Authors: Wang Chao , Song Shuguang , Niu Yaoling , Wei Chunjing , Su Li
Published: October 2016

As the major component, Archean granitoids provide us with an insight into the formation of the early continental crust. We report the study of a series of Neoarchean granitoids, including tonalite–trondhjemite–granodiorite (TTG) and potassic granitoids, in the Xingcheng region of the eastern North China Craton. Zircon U–Pb dating shows that the TTG granitoids were emplaced in the Neoarchean within a 75 Myr period (2595–2520 Ma), with coeval mafic magmatic enclaves, followed by intrusion of potassic granitoids. The geochemistry of the TTG granitoids is consistent with partial melting of Mesoarchean enriched mafic crustal sources at different depths (up to 10–12 kbar equivalent pressure) during a continental collision event. The potassic granitoids are derived from either low-degree melting of Mesoarchean enriched mafic crustal sources or remelting of Mesoarchean TTGs in response to post-collisional extension, and were hybridized with Neoarchean mantle-derived mafic melts to various degrees. The TTG and potassic granitoids in the Xingcheng region record the evolution from collision of micro-continental blocks to post-collisional extension, consistent with other studies, suggesting that the amalgamation of micro-continental blocks is what gave rise to the cratonization of the North China Craton at the end of the Archean. The rock assemblage of these granitoids resembles those of syn- and post-collisional magmatism in Phanerozoic orogenic belts, and the estimated average composition is similar to that of the present-day upper continental crust, suggesting that a prototype upper continental crust might have been developed at the end of the Archean from a mixture of TTG and potassic granitoids. Together with concurrent high-grade metamorphism in the North China Craton, we conclude that collisional orogenesis is responsible for continental cratonization at the end of the Archean in the North China Craton.
A Calcium-in-Olivine Geohygrometer and its Application to Subduction Zone Magmatism
Authors: Gavrilenko Maxim , Herzberg Claude , Vidito Christopher , Carr Michael J. , Tenner Travis , Ozerov Alexey
Published: October 2016

High-precision electron microprobe analyses were obtained on olivine grains from Klyuchevskoy, Shiveluch and Gorely volcanoes in the Kamchatka Arc; Irazú, Platanar and Barva volcanoes of the Central American Arc; and mid-ocean ridge basalt (MORB) from the Siqueiros Transform. Calcium contents of these subduction zone olivines are lower than those for olivines from modern MORB, Archean komatiite and Hawaii. A role for magmatic H2O is likely for subduction zone olivines, and we have explored the suggestion of earlier workers that it has affected the partitioning of CaO between olivine and silicate melt. We provide a provisional calibration of DCaOOl/L as a function of magmatic MgO and H2O, based on nominally anhydrous experiments and minimally degassed H2O contents of olivine-hosted melt inclusions. Application of our geohygrometer typically yields 3–4 wt % magmatic H2O at the Kamchatka and Central American arcs for olivines having ∼1000 ppm Ca, which agrees with H2O maxima from melt inclusion studies; Cerro Negro and Shiveluch volcanoes are exceptions, with about 6% H2O. High-precision electron microprobe analyses with 10–20 μm spatial resolution on some olivine grains from Klyuchevskoy and Shiveluch show a decrease in Ca content from the core centers to the rim contacts, and a sharp increase in Ca in olivine rims. We suggest that the zoning of Ca in olivine from subduction zone lavas may provide the first petrological record of temporal changes that occur during hydration of the mantle wedge and dehydration during ascent, and we predict olivine H2O contents that can be tested by secondary ionization mass spectrometry analysis.
Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer’s disease
Authors: Lu Qiongshi , Powles Ryan L. , Abdallah Sarah , Ou Derek , Wang Qian , Hu Yiming , Lu Yisi , Liu Wei , Li Boyang , Mukherjee Shubhabrata , Crane Paul K. , Zhao Hongyu
Published: October 2016

Continuing efforts from large international consortia have made genome-wide epigenomic and transcriptomic annotation data publicly available for a variety of cell and tissue types. However, synthesis of these datasets into effective summary metrics to characterize the functional non-coding genome remains a challenge. Here, we present GenoSkyline-Plus, an extension of our previous work through integration of an expanded set of epigenomic and transcriptomic annotations to produce high-resolution, single tissue annotations. After validating our annotations with a catalog of tissue-specific non-coding elements previously identified in the literature, we apply our method using data from 127 different cell and tissue types to present an atlas of heritability enrichment across 45 different GWAS traits. We show that broader organ system categories (e.g. immune system) increase statistical power in identifying biologically relevant tissue types for complex diseases while annotations of individual cell types (e.g. monocytes or B-cells) provide deeper insights into disease etiology. Additionally, we use our GenoSkyline-Plus annotations in an in-depth case study of late-onset Alzheimer’s disease (LOAD). Our analyses suggest a strong connection between LOAD heritability and genetic variants contained in regions of the genome functional in monocytes. Furthermore, we show that LOAD shares a similar localization of SNPs to monocyte-functional regions with Parkinson’s disease. Overall, we demonstrate that integrated genome annotations at the single tissue level provide a valuable tool for understanding the etiology of complex human diseases. Our GenoSkyline-Plus annotations are freely available athttp://genocanyon.med.yale.edu/GenoSkyline.

Author Summary

After years of community efforts, many experimental and computational approaches have been developed and applied for functional annotation of the human genome, yet proper annotation still remains challenging, especially in non-coding regions. As complex disease research rapidly advances, increasing evidence suggests that non-coding regulatory DNA elements may be the primary regions harboring risk variants in human complex diseases. In this paper, we introduce GenoSkyline-Plus, a principled annotation framework to identify tissue and cell type-specific functional regions in the human genome through integration of diverse high-throughput epigenomic and transcriptomic data. Through validation of known non-coding tissue-specific regulatory regions, enrichment analyses on 45 complex traits, and an in-depth case study of neurodegenerative diseases, we demonstrate the ability of GenoSkyline-Plus to accurately identify tissue-specific functionality in the human genome and provide unbiased, genome-wide insights into the genetic basis of human complex diseases.
Optimized CRISPR–Cas9 System for Genome Editing in Zebrafish
Authors: Vejnar Charles E. , Moreno-Mateos Miguel A. , Cifuentes Daniel , Bazzini Ariel A. , Giraldez Antonio J.
Published: October 2016

This protocol describes how to generate and genotype mutants using an optimized CRISPR–Cas9 genome-editing system in zebrafish (CRISPRscan). Because single guide RNAs (sgRNAs) have variable efficiency when targeting specific loci, our protocol starts by explaining how to use the web tool CRISPRscan to design highly efficient sgRNAs. The CRISPRscan algorithm is based on the results of an integrated analysis of more than 1000 sgRNAs in zebrafish, which uncovered highly predictive factors that influence Cas9 activity. Next, we describe how to easily generate sgRNAs in vitro, which can then be injected in vivo to target specific loci. The use of highly efficient sgRNAs can lead to biallelic mutations in the injected embryos, causing lethality. We explain how targeting Cas9 to the germline increases viability by reducing somatic mutations. Finally, we combine two methods to identify F1 heterozygous fish carrying the desired mutations: (i) Mut-Seq, a method based on high-throughput sequencing to detect F0 founder fish; and (ii) a polymerase chain reaction–based fragment analysis method that identifies F1 heterozygous fish characterized by Mut-Seq. In summary, this protocol includes the steps to generate and characterize mutant zebrafish lines using the CRISPR–Cas9 genome engineering system.
Detection of DNA Fragmentation in Apoptotic Cells by TUNEL
Authors: Crowley Lisa C. , Marfell Brooke J. , Waterhouse Nigel J.
Published: October 2016

Degradation of DNA into oligonucleosomal-sized fragments is a unique event in apoptosis that is orchestrated by caspase-activated DNase. Traditionally, this event is observed by resolving cellular DNA by gel electrophoresis, which results in a characteristic “ladder” pattern. However, this technique is time-consuming and cannot be used to quantitate the number of apoptotic cells in a sample. Terminal dUTP nick-end labeling (TUNEL) of fragmented DNA allows researchers to identify DNA fragmentation at the single-cell level. This method involves the specific addition of fluorescently labeled UTP to the 3′-end of the DNA fragments by terminal deoxynucleotidyl transferase. The TUNEL assay is both fast and sensitive. Here, we describe a protocol in which cells are treated with TUNEL reagent and counterstained with Hoechst 33342. In contrast to TUNEL, which only stains apoptotic cells, Hoechst 33342 stains the DNA of all cells.
Characterization of Protein–Protein Interactions Using Protein Microarrays
Authors: Paul Corry , Rho HeeSool , Neiswinger Johnathan , Zhu Heng
Published: October 2016

Functional protein microarrays allow fast, straightforward, and efficient high-throughput screening of protein–protein interactions. The microarray approach has outpaced other interaction methods, such as yeast two-hybrid screens, in part because of the vast amounts of information that can be obtained during a single assay. This protocol describes how to perform a binding assay for a protein of interest using a proteome microarray composed of thousands of functional, recombinant proteins adhered to a microchip.
Characterization of Lipid–Protein Interactions Using Nonquenched Fluorescent Liposomal Nanovesicles and Yeast Proteome Microarrays
Authors: Lu Kuan-Yi , Chen Chien-Sheng , Neiswinger Johnathan , Zhu Heng
Published: October 2016

Studying lipid–protein interactions is central to understanding lipid signaling, a key regulatory system in cells. To better identify lipid-binding proteins, we developed a nonquenched fluorescent (NQF) liposome that is able to carry both fluorescent molecules and a lipid of interest. By combining the strength of NQF liposomes with protein microarray technology, the method presented here facilitates high-throughput screening of lipid–protein interactions. This protocol describes how to prepare NQF liposomes and apply the fabricated liposomes to yeast proteome microarrays.
Posttranslational Modification Assays on Functional Protein Microarrays
Authors: Neiswinger Johnathan , Uzoma Ijeoma , Cox Eric , Rho HeeSool , Jeong Jun Seop , Zhu Heng
Published: October 2016

Protein microarray technology provides a straightforward yet powerful strategy for identifying substrates of posttranslational modifications (PTMs) and studying the specificity of the enzymes that catalyze these reactions. Protein microarray assays can be designed for individual enzymes or a mixture to establish connections between enzymes and substrates. Assays for four well-known PTMs—phosphorylation, acetylation, ubiquitylation, and SUMOylation—have been developed and are described here for use on functional protein microarrays. Phosphorylation and acetylation require a single enzyme and are easily adapted for use on an array. The ubiquitylation and SUMOylation cascades are very similar, and the combination of the E1, E2, and E3 enzymes plus ubiquitin or SUMO protein and ATP is sufficient for in vitro modification of many substrates.
Reporter Gene Silencing Assays in Fission Yeast
Authors: Cam Hugh P. , Whitehall Simon
Published: October 2016

Reporter gene silencing assays provide a facile method for assessing the function of heterochromatin in Schizosaccharomyces pombe. They use strains containing auxotrophic markers (commonly ura4+ or ade6+) located within a heterochromatic region. Transcriptional silencing of these reporters can be assessed by plating serial dilutions of cells onto minimal agar. In addition, silencing of ura4+ renders cells resistant to 5-fluoroorotic acid (5-FOA) and ade6+ silencing results in red colony color on adenine-limiting agar. Various reporters for each of the major heterochromatic domains (telomeres, centromeres, and the mating type locus) are available and, importantly, transcriptional silencing is correlated with the proper function of these regions.
High-Throughput Yeast Strain Sequencing
Authors: Schwartz Katja , Sherlock Gavin
Published: October 2016

The original yeast genome sequencing project was a monumental task, spanning several years, which resulted in the first sequenced eukaryotic genome. The 12 Mbp reference sequence was generated from yeast strain S288c and was of extremely high quality. In the years since it was published, sequencing technology has advanced apace, such that it is within the reach of most labs to sequence yeast strains of interest almost as a matter of standard practice, either via core facilities at their institution or through commercial sequencing services. Because of the availability of the high-quality reference sequence (which itself has received approximately 1500 updates derived from high-throughput sequencing data), reliable identification of differences between a strain of interest and the reference is relatively straightforward, at least for the nonrepetitive regions of the genome. In this introduction, we describe current high-throughput sequencing technology and methods for analysis of the resulting data.
Optimization Strategies for the CRISPR–Cas9 Genome-Editing System
Authors: Vejnar Charles E. , Moreno-Mateos Miguel A. , Cifuentes Daniel , Bazzini Ariel A. , Giraldez Antonio J.
Published: October 2016

The CRISPR–Cas9 system uncovered in bacteria has emerged as a powerful genome-editing technology in eukaryotic cells. It consists of two components—a single guide RNA (sgRNA) that directs the Cas9 endonuclease to a complementary DNA target site. Efficient targeting of individual genes requires highly active sgRNAs. Recent efforts have made significant progress in understanding the sequence features that increase sgRNA activity. In this introduction, we highlight advancements in the field of CRISPR–Cas9 targeting and discuss our web tool CRISPRscan, which predicts the targeting activity of sgRNAs and improves the efficiency of the CRISPR–Cas9 system for in vivo genome engineering.
The liability for employers for the conduct of their employees – when does an employee’s conduct fall within the “the course of employment”?
Authors: Mustafa Engin
Published: October 2016

Purpose

This paper aims to review the latest management developments across the globe and pinpoint practical implications from cutting-edge research and case studies.

Design/methodology/approach

This briefing is prepared by an independent writer who adds their own impartial comments and places the papers in context.

Findings

All employers need to understand the exposure to risk that their organizations face. In the field of human resource management, the liability of the employer for the actions (or omissions) of an employee is a key part of managing that risk. The scope of such liability is delimited by both statute and case law which has helped clarify the position of employer liability, thereby allowing an employer to mitigate risk.

Practical implications

The paper provides strategic insights and practical thinking that have influenced some of the world’s leading organizations.

Originality/value

The briefing saves busy executives and researchers hours of reading time by selecting only the very best, most pertinent information and presenting it in a condensed and easy-to-digest format.