bluuebunny/crossref_metadata_2025 huggingface dataset:
Modified propagation path and expanded coupling regime of lower hybrid fast wave by n∥-upshift via wave scattering in VEST
Authors: Jo JongGab , Wang J. , Kim S. C. , Hong SeulChan , Lim Soobin , Yang J. , Kim S. H. , Hwang Y. S.
Published: January 2019

Experimental investigation of lower hybrid fast wave (LHFW) coupling and propagation is carried out by wave measurements utilizing magnetic probes in Versatile Experiment Spherical Torus. Coupling experiments are conducted in marginal (ne≥nconfluence) and prohibited (ne≫nconfluence) regimes for fast wave coupling. In the marginal regime of Ip = 25 kA, about two folds of n∥-upshift are observed. The propagation path of the fast wave is largely modified compared to that of full wave simulation, and more fast waves are detected inside the last-closed-flux surface despite the unsatisfied accessibility condition. Since spectral broadening is measured to be narrow and linearly proportional to coupled wave power with a high density fluctuation of about 20% in the frequency range (ω0/ωlh∼15), it is thought to be crucially correlated with wave scattering rather than parametric decay instabilities. Consequently, the spectral broadening implicates that n∥-upshift can take place via a wave scattering mechanism. In the prohibited regime of Ip = 100 kA, more enhanced coupling of up to 90% is observed with similar density fluctuation to that of the marginal regime, which is explained with intensified wave scattering due to the high dielectric constant of spherical torus plasmas. It is concluded that practical windows for propagation and coupling of LHFW are widened with the aid of n∥-upshift via wave scattering even though the accessibility condition is not satisfied right in front of the antenna.
Temperature gradients for thermophysical and thermochemical property measurements to 3000 °C for an aerodynamically levitated spheroid
Authors: McCormack Scott J. , Tamalonis Anthony , Weber Richard J. K. , Kriven Waltraud M.
Published: January 2019

This study examines thermal gradients in ceramic oxide spheroids being aerodynamically levitated in a conical nozzle levitator (CNL) system equipped with a CO2 laser (10.6 µm wavelength). The CNL system is a versatile piece of equipment that can easily be coupled with advanced thermophysical and thermochemical measuring devices, such as diffraction/scattering (X-ray and neutron), nuclear magnetic resonance, and calorimetry, for the analysis of bulk spheroidal solids and liquids. The thermal gradients of a series of single crystal, polycrystalline solids, and liquid spheroids have been measured spatially in the CNL system, by means of a disappearing filament pyrometer (800–3000 °C) and by X-ray diffraction with reference to an internal standard (Pt: 800–1600 °C). The thermal gradient in a levitated sample being heated by a laser from the top can be minimized by: (i) maximizing the sphericity, (ii) maximizing the density, and (iii) minimizing microstructural features. A spheroid with these properties can be manufactured via machining a perfect sphere from a highly dense, chemically and phase pure pellet. These properties promote rotation of the sample about multiple axes in the air stream, enabling homogeneous heating. This homogeneous heating is the dominant factor in reducing thermal gradients in solid state samples. It was found that the thermal gradient in an ∼3 mm diameter solid sample could be reduced from 1000 °C to 30 °C, by having a perfectly spherical shape that could rotate on multiple axes in a high velocity gas stream (∼1500–2000 cm3/min). These findings will allow accurate thermophysical and thermochemical property measurements of solids in situ at high temperatures, using the CNL system.
Schottky barrier height modulation of metal–interlayer–semiconductor structure depending on contact surface orientation for multi-gate transistors
Authors: Kim Gwang-Sik , Lee Tae In , Cho Byung Jin , Yu Hyun-Yong
Published: January 2019

A metal–interlayer–semiconductor (MIS) structure that is realized by inserting an ultrathin interlayer between a contact metal and a semiconductor has been investigated recently as a low-resistance non-alloyed contact structure. However, a comprehensive and systematical investigation of Schottky barrier height (SBH) modulation through the insertion of an interlayer depending on the contact surface orientation has not been conducted despite its importance for its use in multi-gate transistors. Therefore, in this work, the SBH modulation of the MIS contact structure for different contact surface orientations is systematically investigated, and a comprehensive analysis platform of the MIS contact structure is suggested. Two factors, (1) alleviation of Fermi-level pinning due to metal-induced gap states and interface states and (2) formation of the interface dipole, contribute to the SBH modulation in the MIS contact structure. Their contributions depending on the contact surface orientation are evaluated through a comparison of the contact structures on (100)- and (110)-oriented germanium (Ge). These factors and how they should be considered for a certain contact surface in Ge-channel multi-gate transistors are investigated. The investigation and the proposed analysis platform will contribute to the design of high-performance non-alloyed contact schemes for next-generation multi-gate transistors.
Void collapse generated meso-scale energy localization in shocked energetic materials: Non-dimensional parameters, regimes, and criticality of hotspots
Authors: Rai N. K. , Udaykumar H. S.
Published: January 2019

The formation of hotspots due to collapse of voids leads to enhanced sensitivity of heterogeneous energetic (HE) materials. Several mechanisms of void collapse have been identified, but the regimes in which these mechanisms dominate have not been clearly delineated using scaling arguments and dimensionless parameters. This paper examines void collapse in cyclotetramethylene-tetranitramine (HMX) to demarcate regimes where plastic collapse and hydrodynamic jetting play dominant roles in influencing hotspot related sensitivity. Using scaling arguments, a criticality envelope for HMX is derived in the form Σcr=∑(Ps,Dvoid), i.e., as a function of shock pressure Ps and void size Dvoid, which are controllable design parameters. Once a critical hotspot forms, its subsequent growth displays a complex relationship to Ps and Dvoid. These complexities are explained with scaling arguments that clarify the physical mechanisms that predominate in various regimes of hotspot formation. The insights and scaling laws obtained can be useful in the design of HE materials.
Quantized plasmon excitations of electron gas in potential well
Authors: Akbari-Moghanjoughi M.
Published: January 2019

Using the Schrödinger-Poisson system in this paper, the basic quantum features of plasmon excitations in a free noninteracting electron gas with arbitrary degeneracy are investigated. The standing wave solution of the free electron gas is derived from the corresponding linearized pseudo-force system with appropriate boundary conditions. It is shown that the plasmon excitation energies for electron gas confined in an infinite potential well are quantized eigenvalues of which are obtained. It is found that any arbitrary degenerate quantum electron gas possesses two different characteristic length scales, unlike the classical dilute electron gas, with the smaller length scale corresponding to the single particle oscillation and the larger one due to the collective Langmuir excitations. The probability density of the free electron gas in a box contains fine structures which are modulated over a larger pattern. The envelope probability density profile for the electron Fermi gas confined in an impenetrable well in different energy states is found to be quite similar to that of the free electron confined to an infinite potential well. However, the illustrative features of the plasmon theory presented in this research can be further elaborated in order to illuminate a wide range of interesting physical phenomena involving both the single particle and the collective features.
Pasture condition and milk production by grazing dairy cows as affected by daily herbage-allowance restriction
Authors: Merino V. M. , Balocchi O. A. , Pulido R. G.
Published: January 2019

Daily herbage allowance is recognised as the main tool to control pasture utilisation and milk production per cow. The aim of the present study was to evaluate the long-term effects of daily herbage allowance (DHA) on pasture characteristics and milk production of dairy cows. Forty-four dairy cows were randomly assigned to one of four treatments in a 2 × 2 factorial design by considering two levels of DHA (20 and 30 kg DM/cow.day) and two types of supplements (high-moisture maize and maize silage) over a 77-day period. Pre- and post-grazing herbage masses, vertical distribution of herbage mass, species density, botanical and chemical composition, sward depletion and changes in morphological components of the pasture were measured. The effect of DHA on soil compaction was evaluated on the basis of the penetration resistance. Milk production and composition levels, bodyweights and body condition scores were recorded. Post-grazing residual declined as the level of DHA decreased, while grazing efficiency increased from 39.8% to 44.8%. We found no effects of DHA on any pasture characteristics, pasture regrowth or soil compaction. Low-DHA conditions induced a faster sward-height reduction, while the herbage mass remained unaffected. Individual milk production decreased with DHA. However, milk outputs per hectare increased by 2772 L/ha. Milk composition, bodyweight and body condition score were not affected by DHA. The results showed that DHA restriction decreases milk production per cow while increasing both herbage utilisation and milk production per hectare, without affecting long-term pasture condition.
Non-additive effects of alternative stable states on landscape flammability in NW Patagonia: fire history and simulation modelling evidence
Authors: Tiribelli Florencia , Morales Juan Manuel , Gowda Juan Haridas , Mermoz Mónica , Kitzberger Thomas
Published: January 2019

Understanding the relationship between flammability and time since fire (TSF) is crucial for predicting ecosystem responses to changes in fire regimes. Landscapes composed of alternative stable states displaying positive fire–vegetation feedbacks are especially sensitive to these changes. We derived TSF–flammability functions (Logistic, Olson, Moisture, Weibull) from survival analysis applied to north-west Patagonian landscapes and simulated landscapes composed of different proportions of alternative stable states (shrublands and forest) and fire frequencies. We expected that landscapes dominated by shrublands would show an asymptotic growth (Logistic or Olson) and those dominated by forest would show a hump-shaped growth (Moisture). Additionally, we expected that the landscape-level flammability functions would resemble the pattern of the most abundant community. We found that shrublands tended to dominate the TSF–flammability relationship (Logistic) even when they were less abundant in the landscape (non-additive effects). The flammability function followed a hump-shaped growth (Moisture) only when the forest cover was >80%. Our results highlight that alternative stable states occur not only because of positive fire–vegetation feedbacks, but also thanks to the non-additivity of the flammability of the different states in the landscape. Non-additive effects could have an important role in accelerating landscape transformations towards more flammable states.
Multidrug-resistant plasmids repress chromosomally encoded T6SS to enable their dissemination
Authors: Di Venanzio Gisela , Moon Ki Hwan , Weber Brent S. , Lopez Juvenal , Ly Pek Man , Potter Robert F. , Dantas Gautam , Feldman Mario F.
Published: January 2019

Acinetobacter baumannii
(
Ab
) is a nosocomial pathogen with one of the highest rates of multidrug resistance (MDR). This is partially due to transmissible plasmids. Many
Ab
strains harbor a constitutively active type VI secretion system (T6SS) that is employed to kill nonkin bacteria. T6SS and plasmid conjugation both involve cell-to-cell contact. Paradoxically, successful conjugation requires the survival of the recipient, which is the target of the T6SS. Thus, an active T6SS in either the donor or the recipient poses a challenge to plasmid conjugation. Here, we show that large conjugative MDR plasmids heavily rely on their distinctive ability to repress the T6SS of their hosts to enable their own dissemination and the conjugation of other plasmids, contributing to the propagation of MDR among
Acinetobacter
isolates.
(Im)politeness, morality and the internet
Authors: Xie Chaoqun
Published: January 2019

Much recent research has contributed to the emergence of a moral turn in (im)politeness research, further confirming the evaluative nature of (im)politeness and the moral basis of (im)politeness evaluations, and further illuminating, among other things, what is really at work when (im)politeness evaluations take place, what the moral order consists of and how the moral order influences (im)politeness evaluations. Meanwhile, thanks to much emphasis on the instrumentality of words and utterances, a distinction can be discerned between ‘politeness without’ (or practical politeness) and ‘politeness within’ (or true politeness). Politeness within is true and truthful, but politeness without is not necessarily so. True politeness may be in when self is out. This special issue aims to further foreground the link between (im)politeness and morality in people’s online interactions, revealing something about ourselves and about our life-worlds.
The personal and/as the political
Authors: Georgakopoulou Alex , Vasilaki Maria
Published: January 2019

Drawing on our previous work on the role of small stories in social-mediatized engagements with the Greek socio-economic crisis (Georgakopoulou 2014,2015), in this article, we set out to shed light on impoliteness on social media through the lens of small stories research. We explore how Facebook and YouTube commenters “bash” political leaders and perceived political opponents and attribute blame to them for the crisis, through comments that attest to specific links of doing impoliteness with storying the crisis. Bashing has been previously related to the affective reactions of participants in online comments on current affairs. In this case, we bring to the fore a salient combination in our data of (mainly on-record) impoliteness strategies for bashing politicians with specific narrating positions in stories about the crisis: the narrator as sufferer, as witness of suffering, and as spokesperson for collective suffering. We argue that in all these cases, on-record impoliteness is normally placed at the end of a small story and presented as legitimated and justified by the preceding account. We conclude with the implications of the association of impoliteness targeting public figures with social-mediatized processes of personalizing and constructing expertise on the basis of experience on the one hand and, on the other hand, of jointly (re)asserting moral order in political affairs.
“Ya bloody drongo!!!”
Authors: Sinkeviciute Valeria
Published: January 2019

This paper explores impoliteness-related discourse on Facebook as a form of expressing situated moral judgement. The analysis focuses on negative and aggressive comments as a response to one public post that claims the non-existence of Australia. The content of the post indicates the threat to national identity of anyone who associates themselves with the country. As a result, a large number of impolite comments were made. A qualitative analysis of the dataset (limited to one month from the post’s publication) reveals four main strategies that are used in order to express the judgement of the post’s inappropriateness and repair the wrongdoing. Those range from insults of the author’s mental abilities and suspicion of drug use to violence-related discourse (e.g., death threats) and counter-attack of the author’s national identity. This paper, thus, aims to contribute to a growing area of research into online impoliteness.
Impoliteness online
Authors: Kienpointner Manfred
Published: January 2019

This paper provides an overview of the strategies and techniques of hate speech in online discourse (on online discourse or computer-mediated communication in general cf. e.g.,Schwarzhaupt-Scholz 2004;Schmidt 2013;Dittler and Hoyer 2014; Seargeant and Tagg 2014). Based on a collection of online texts belonging to different genres (discussion forums, blogs, social media, tweets, homepages), this paper will provide a qualitative analysis of destructively impolite utterances in online interactions. This analysis will make use of the standard typologies of impoliteness and their recent extensions (such asCulpeper 1996,2005,2011;Kienpointner 1997,2008;Kleinke and Bös 2015), but some modifications and elaborations of these typologies will also be taken into account. Moreover, social, cultural and political reasons for the recent dramatic increase in hate speech in online interactions will be explored. Finally, the problem of how to deal with this destructive use of language will be briefly discussed and some possible solutions will be suggested (cf.Banks 2010).
Translanguaging in culturally sustaining systemic functional linguistics
Authors: Khote Nihal , Tian Zhongfeng
Published: January 2019

In today’s globalized multilingual classrooms, deficit ideologies tend to disregard the cultural capital and mobile semiotic resources that immigrant and culturally diverse students bring with them (Blommaert 2010). There is a growing need to focus on culturally sustaining pedagogies that reframe how we think about teaching multilingual learners (Paris and Alim 2017). By bringing two perspectives – Halliday’s systemic functional linguistics (SFL) (Halliday 1993) theory andGarcía’s (2009)notion of translanguaging – into dialogue, we explore their conceptual alignments and complementarities. Building upon this, we envision culturally sustaining SFL as an integrative framework which holds the promise of fostering meaningful heteroglossic contexts of learning for multilingual learners in supporting their multiliteracies (seeKhote 2017;Harman and Khote 2018). Data from one of the author’s English Language Arts (ELA) classroom will further illustrate: (a) how students’ complex linguistic repertoires were mobilized as a foundational resource for developing disciplinary literacy, and (b) how multilingual students engaged with the curriculum to interrogate discourses that diminish their authentic participation in the classroom.
Convergences and alignments between translanguaging and critical literacies work in bilingual
classrooms
Authors: Lau Sunny Man Chu
Published: January 2019

Translanguaging pedagogy, stemming from a dynamic view of bilingualism, aims to creatively mobilize students’
plural communicative repertoires for meaningful learning and destabilize hegemonic discourses about minoritized students and
languages. It espouses in itself a criticality that raises awareness of the inequitable and arbitrary nature of language
hierarchy, separation and marginalization for social justice purposes, a central tenet shared with critical literacy (CL)
education. This paper explores the convergences and alignments between translanguaging pedagogy and CL and the affordances for
critical bilingual learning when employed together. To examine the synergies between translanguaging and CL, I use Janks’ (2010) synthesis CL model to tease out their interconnections as well as their
transformative potential when used jointly in bilingual classrooms. Elaborating on key literacy events from a CL project with
emergent bilingual students, this paper illustrates how translanguaging opens up spaces for rigorous language and CL
engagement.
Intersection theory of toric 𝑏-divisors in toric varieties
Authors: Botero Ana
Published: January 2019

We introduce toricbb-divisors on complete smooth toric varieties and a notion of integrability of such divisors. We show that under some positivity assumptions toricbb-divisors are integrable and that their degree is given as the volume of a convex set. Moreover, we show that the dimension of the space of global sections of a nef toricbb-divisor is equal to the number of lattice points in this convex set and we give a Hilbert–Samuel-type formula for its asymptotic growth. This generalizes classical results for classical toric divisors on toric varieties. Finally, we relate convex bodies associated tobb-divisors with Newton–Okounkov bodies. The main motivation for studying toricbb-divisors is that they locally encode the singularities of the invariant metric on an automorphic line bundle over a toroidal compactification of a mixed Shimura variety of non-compact type.
What Is the Relationship between Worker Skills and Outcomes for Families in Child and Family Social Work?
Authors: Forrester Donald , Westlake David , Killian Mike , Antonopolou Vivi , McCann Michelle , Thurnham Angela , Thomas Roma , Waits Charlotte , Whittaker Charlotte , Hutchison Douglas
Published: January 2019

Communication skills are fundamental to social work, yet few studies have directly evaluated their impact. In this study, we explore the relationship between skills and outcomes in 127 families. An observation of practice was undertaken on the second or third meeting with a family. Practice quality was evaluated in relation to seven skills, which were grouped into three dimensions: relationship building, good authority and evocation of intrinsic motivation. Outcomes at approximately six months were parent-reported engagement (Working Alliance Inventory), Goal Attainment Scaling (GAS), an eleven-point family life satisfaction rating, the Family Environment Scale and General Health Questionnaire and service outcomes from agency records including children entering care. Relationship-building skills predicted parent-reported engagement, although good authority and evocation had stronger relationships with outcome measures. Where workers visited families more often, relationships between skills and outcomes were stronger, in part because workers had more involvement and in part because these families were more likely to have significant problems. The relationship between skills and outcomes was complicated, although the findings provide encouraging evidence that key social work skills have an influence on outcomes for families.
Diminished Locomotor Control Is Associated With Reduced Neurovascular Coupling in Older Adults
Authors: Jor’dan Azizah J , Manor Brad , Iloputaife Ikechukwu , Habtemariam Daniel A , Bean Jonathan F , Sorond Farzaneh A , Lipsitz Lewis A
Published: January 2019

Background

Walking, especially while dual-tasking, requires functional activation of cognitive brain regions and their connected neural networks. This study examined the relationship between neurovascular coupling (NVC), as measured by the change in cerebral blood flow in response to performing a cognitive executive task, and dual-task walking performance.

Methods

Seventy community-dwelling older adults aged 84 ± 5 years within the Maintenance of Balance, Independent Living, Intellect and Zest in the Elderly (MOBILIZE) Boston Study were divided into LOW (n = 35) and HIGH (n = 35) NVC. NVC was quantified by transcranial Doppler ultrasound and stratified by the median change in cerebral blood flow velocity of the middle cerebral artery induced by the performance of the n-back task of executive function. Walking metrics included walking speed, step width, stride length, stride time, stride time variability, and double-support time from single- and dual-task walking conditions, as well as the “cost” of dual-tasking.

Results

During both single- and dual-task walking, older adults with LOW NVC displayed narrower step width (p = .02 and p = .02), shorter stride length (p = .01 and p = .02), and longer double-support time (p = .03 and p = .002) when compared with the HIGH group. During single-task walking only, LOW NVC was also linked to slower walking speed (p = .02). These associations were independent of age, height, hypertension, atrial fibrillation, and assistive device. The LOW and HIGH NVC groups did not differ in dual-task costs to walking performance.

Conclusion

In older adults, diminished capacity to regulate cerebral blood flow in response to an executive function task is linked to worse walking performance under both single- and dual-task conditions, but not necessarily dual-task costs.
Executive Function and Subjective Well-being in Middle and Late Adulthood
Authors: Toh Wei Xing , Yang Hwajin , Hartanto Andree
Published: January 2019

Objectives

A growing body of research has investigated psychosocial predictors of subjective well-being (SWB), a key component of healthy aging, which comprises life satisfaction and affective well-being. However, few studies have examined how executive function (EF)—a collection of adaptive, goal-directed control processes—could affect SWB in middle and late adulthood.

Methods

By analyzing a nationally representative adult cohort ranging from the early 30s to early 80s from the Midlife Development in the United States 2 study, we examined two potential mediators (i.e., sense of control vs positive reappraisal) that could underlie the relation between EF and SWB. Further, we assessed how these mediational pathways would differ across midlife and older adulthood.

Results

Our results revealed that sense of control, but not positive reappraisal, significantly mediated the relation between EF and life satisfaction and affective well-being. Moreover, these mediation effects were significantly moderated by age, with more pronounced effects among older adults.

Discussion

We found that EF in later adulthood facilitates a sense of control over obstacles that interfere with the attainment of goals, which in turn is associated with greater life satisfaction and positive affect. This underscores the role of EF as an increasingly valuable resource that buffers against declines in sense of control and SWB in late adulthood.
Asymptotic analysis of drug dissolution in two layers having widely differing diffusivities
Authors: Vynnycky Michael , McKee Sean , Meere Martin , McCormick Christopher , McGinty Sean
Published: January 2019

This paper is concerned with a diffusion-controlled moving boundary problem in drug dissolution, in which the moving front passes from one medium to another for which the diffusivity is many orders of magnitude smaller. The classical Neumann similarity solution holds while the front is passing through the first layer, but this breaks down in the second layer. Asymptotic methods are used to understand what is happening in the second layer. Although this necessitates numerical computation, one interesting outcome is that only one calculation is required, no matter what the diffusivity is for the second layer.
Pro: Vascular access surveillance in mature fistulas: is it worthwhile?
Authors: Tessitore Nicola , Poli Albino
Published: January 2019

Guidelines recommend regular screening of mature arteriovenous fistulas (AVFs) for preemptive repair of significant stenosis (≥50% lumen reduction) at high risk of thrombosis, identifiable from clinical signs of access dysfunction (monitoring) or by measuring access blood flow (Qa surveillance), which also enables stenosis detection in functional accesses. To compare the value of Qa surveillance versus monitoring, a meta-analysis was performed on the randomized controlled trials (RCTs) comparing the two screening strategies. It emerged that correcting stenosis identified by Qa surveillance significantly halved the risk of thrombosis [relative risk (RR) = 0.51, 95% confidence interval (CI) 0.35–0.73] and access loss (RR = 0.47, 95% CI 0.28–0.80) in comparison with intervention prompted by clinical signs of access dysfunction. One small RCT aiming to identify an optimal Qa threshold showed that stenosis repair at Qa >500 mL/min produced a significant 3-fold reduction in the risk of thrombosis (RR = 0.37, 95% CI 0.12–0.97) and access loss (RR = 0.36, 95% CI 0.09–0.99) in comparison with intervening when Qa dropped to <400 mL/min as per guidelines. To test the real-world benefits of Qa surveillance, the expected RCT-based thrombosis and access loss rates with Qa surveillance were compared with the rates with monitoring reported in observational studies: the expected thrombosis and access loss rates with surveillance were only lower than with monitoring when a Qa >500 mL/min was considered (2.4, 95% CI 1.0–4.6 and 2.2, 95% CI 0.7–5.0 versus 9.4, 95% CI 7.4–11.3 and 10.3, 95% CI 7.7–13.4 events per 100 AVFs-year, P ≤ 0.024), suggesting that in clinical practice adopting Qa surveillance may only be worthwhile at centres with high thrombosis and access loss rates associated with monitoring, and adopting Qa thresholds >500 mL/min for elective stenosis repair.
The ideational foundations of social democratic austerity in the context of the great recession
Authors: Bremer Björn , McDaniel Sean
Published: January 2019

The ‘austerity settlement’ has come to define the post-crisis European political economy. Since 2010, parties from across Europe’s political mainstream have implemented austerity and despite the apparent conflict with the interests of their traditional constituents, even social democratic parties have acquiesced to this settlement. However, within the existing literature ‘social democratic austerity’ is currently under-theorized as it is assumed to involve a rather straightforward adaptation of social democrats to neo- and/or ordoliberal ideas. Utilizing rich and original evidence from over 60 elite interviews with key social democratic stakeholders in France, Germany and the UK, this article contests this view. It demonstrates instead that a distinct set of ideas based on New Keynesianism, supply-side economics, and the social investment paradigm provide the ideational foundations for social democratic austerity post-crisis. Understanding this, it is argued, is critical in order to fully appreciate how and why austerity has become dominant in post-crisis Europe.
Lactobacillus salitolerans sp. nov., a novel lactic acid bacterium isolated from spent mushroom substrates
Authors: Tohno Masanori , Tanizawa Yasuhiro , Kojima Yoichiro , Sakamoto Mitsuo , Nakamura Yasukazu , Ohkuma Moriya , Kobayashi Hisami
Published: January 2019

A taxonomic study of a Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, catalase-negative bacterium, strain YK43T, isolated from spent mushroom substrates stored in Nagano, Japan was performed. Growth was detected at 15–45 °C, pH 5.0–8.5, and 0–10 % (w/v) NaCl. The genomic DNA G+C content of strain YK43T was 43.6 mol%. The predominant fatty acids were C16 : 0, C18 : 1 ω9c and summed feature 8. Based on 16S rRNA gene sequence analysis, the type strains of

Lactobacillus acidipiscis

(sequence similarity, 97.6 %) and

Lactobacillus pobuzihii

(97.4 %) were most closely related to YK43T. The average nucleotide identities were 74.1 % between strain YK43T and

L. acidipiscis

DSM 15836T and 74.0 % between YK43T and

L. pobuzihii

E100301T. Based on a multilocus sequence analysis, comparative genomic analysis and a range of phenotypic and chemotaxonomic characteristics, strain YK43T represents a novel species of the genus

Lactobacillus

, for which the name

Lactobacillus
salitolerans sp. nov. is proposed. The type strain is YK43T (=JCM 31331T = DSM 103433T).
Phosphorylation of mitochondrial matrix proteins regulates their selective mitophagic degradation
Authors: Kolitsida Panagiota , Zhou Jianwen , Rackiewicz Michal , Nolic Vladimir , Dengjel Jörn , Abeliovich Hagai
Published: January 2019

Mitophagy is an important quality control mechanism in eukaryotic cells, and defects in mitophagy correlate with aging phenomena and neurodegenerative disorders. It is known that different mitochondrial matrix proteins undergo mitophagy with very different rates, but to date the mechanism underlying this selectivity at the individual protein level has remained obscure. We now present evidence indicating that protein phosphorylation within the mitochondrial matrix plays a mechanistic role in regulating selective mitophagic degradation in yeast, via involvement of the Aup1 mitochondrial protein phosphatase, as well as two known matrix-localized protein kinases, Pkp1 and Pkp2. By focusing on a specific matrix phosphoprotein reporter, we also demonstrate that phospho-mimetic and non-phosphorylatable point mutations at known phosphosites in the reporter increased or decreased its tendency to undergo mitophagy. Finally, we show that phosphorylation of the reporter protein is dynamically regulated during mitophagy, in an Aup1-dependent manner. Our results indicate that structural determinants on a mitochondrial matrix protein can govern its mitophagic fate, and that protein phosphorylation regulates these determinants.

Significance statement

Mitochondrial dysfunction underlies many age-related human pathologies. In normal cells, defective mitochondria are often degraded by mitophagy, a process in which these mitochondria are engulfed in autophagosomes and sent for degradation in the lysosome/vacuole. Surprisingly, studies on mitophagy in diverse eukaryotic organisms reveal an unexpected dimension of protein-level selectivity, wherein individual protein species exhibit divergent rates of mitophagic degradation. In this manuscript, we show that this surprising intra-mitochondrial selectivity can be generated by differential phosphorylation of individual mitochondrial protein species, and we identify mitochondrial phosphatases and kinases which contribute to this regulation. By identifying a mechanism which regulates the intra-mitochondrial selectivity of mitophagic degradation, our findings open the door to potential manipulation of the quality control process in the future.
Long-read sequencing identifies GGC repeat expansion in human-specific NOTCH2NLC associated with neuronal intranuclear inclusion disease
Authors: Sone Jun , Mitsuhashi Satomi , Fujita Atsushi , Mizuguchi Takeshi , Mori Keiko , Koike Haruki , Hashiguchi Akihiro , Takashima Hiroshi , Sugiyama Hiroshi , Kohno Yutaka , Takiyama Yoshihisa , Maeda Kengo , Doi Hiroshi , Koyano Shigeru , Takeuchi Hideyuki , Kawamoto Michi , Kohara Nobuo , Ando Tetsuo , Ieda Toshiaki , Kita Yasushi , Kokubun Norito , Tsuboi Yoshio , Katsuno Masahisa , Iwasaki Yasushi , Yoshida Mari , Tanaka Fumiaki , Suzuki Ikuo K. , Frith Martin C , Matsumoto Naomichi , Sobue Gen
Published: January 2019

Neuronal intranuclear inclusion disease (NIID) is a progressive neurodegenerative disease characterized by eosinophilic hyaline intranuclear inclusions in neuronal and somatic cells. The wide range of clinical manifestations in NIID makes ante-mortem diagnosis difficult 1–8, but skin biopsy realized its ante-mortem diagnosis 9,10 and many NIID cases have been diagnosed by skin biopsy11,12. Most cases of NIID are sporadic, but several familial cases are known. Using a large NIID family, we conducted linkage mapping, found a 58.1-Mb linked-region at 1p22.1-q21.3 with a maximum logarithm of odds (LOD) score of 4.21, and successfully identified a GGC repeat expansion in the 5’ portion of NOTCH2NLC in all affected members by long-read sequencing, but not in unaffected members. We further found the similar expansions in additional 8 unrelated families with NIID as well as 39 sporadic NIID patients. Repeat-primed PCR consistently detected the GGC repeat expansion in all the familial and sporadic patients diagnosed by skin biopsy, but never in unaffected family members nor 200 controls. This shows that pathogenic changes in a human-specific gene evolutionarily generated by segmental duplication indeed causes a human disease.
EK-DRD: a comprehensive database for drug repositioning inspired by experimental knowledge
Authors: Zhao Chongze , Dai Xi , Li Yecheng , Guo Qingqing , Zhang Jianhua , Zhang Xiaotong , Wang Ling
Published: January 2019

Drug repositioning, or the identification of new indications for approved therapeutic drugs, has gained substantial traction with both academics and pharmaceutical companies because it reduces the cost and duration of the drug development pipeline and it reduces the likelihood of unforeseen adverse events. So far, there has not been a systematic effort to identify such opportunities, in part because of the lack of a comprehensive resource for an enormous amount of unsystematic drug repositioning information to support scientists who could benefit from this endeavor. To address this challenge, we developed a new database, Experimental Knowledge-Based Drug Repositioning Database (EK-DRD) by using text and data mining, as well as manual curation. EK-DRD contains experimentally validated drug repositioning annotation for 1861 FDA-approved and 102 withdrawn small molecule drugs. Annotation was done at four levels, using 70,212 target assay records, 3999 cell assay records, 585 organism assay records, and 8910 clinical trial records. Additionally, approximately 1799 repositioning protein or target sequences coupled with 856 related diseases and 1332 pathways are linked to the drug entries. Our web-based software displays a network for integrative relationships between drugs, their repositioning targets, and related diseases. The database is fully searchable and supports extensive text, sequence, chemical structure, and relational query searches.

Availability

EK-DRD is freely available at http://www.idruglab.com/drd/index.php.

Contact

lingwang@scut.edu.cn.
Molecular Logic of Spinocerebellar Tract Neuron Diversity and Connectivity
Authors: Baek Myungin , Menon Vilas , Jessell Thomas M. , Hantman Adam W. , Dasen Jeremy S.
Published: January 2019

Coordinated motor behaviors depend on feedback communication between peripheral sensory systems and central circuits in the brain and spinal cord. Relay of muscle and tendon-derived sensory information to the CNS is facilitated by functionally and anatomically diverse groups of spinocerebellar tract neurons (SCTNs), but the molecular logic by which SCTN diversity and connectivity is achieved is poorly understood. We used single cell RNA sequencing and genetic manipulations to define the mechanisms governing the molecular profile and organization of SCTN subtypes. We found that SCTNs relaying proprioceptive sensory information from limb and axial muscles are generated through segmentally-restricted actions of specific Hox genes. Loss of Hox function disrupts SCTN subtype-specific transcriptional programs, leading to defects in the connections between proprioceptive sensory neurons, SCTNs, and the cerebellum. These results indicate that Hox-dependent genetic programs play essential roles in the assembly of the neural circuits required for proprioception.
Fungal Communities in Soybean Cyst Nematode-Infested Soil under Long Term Corn and Soybean Monoculture and Crop Rotation
Authors: Strom Noah , Hu Weiming , Haarith Deepak , Chen Senyu , Bushley Kathryn
Published: January 2019

Corn (Zea mays) and soybean (Glycine max) production forms an integral part of economies worldwide, but yields are limited by biotic and abiotic factors associated with short rotations and long-term monocultures. In this study, a long-term rotation study site with corn and soybean planted in annual rotation, five-year rotation, and long-term monoculture was utilized to examine the relationships between crop sequences, soil fungal communities, soybean cyst nematode (SCN, Heterodera glycines) densities, soil properties, and crop yields. High throughput sequencing of the ITS1 region of fungal rDNA revealed that soil fungal community structure varied significantly by crop sequence, with fungal communities under five consecutive years of monoculture becoming progressively similar to communities in long-term monoculture plots associated with their respective crop hosts. Total alpha diversity was greater under corn, but patterns of diversity and relative abundance of specific functional groups differed by crop host, with more pathotrophs proliferating under soybean and more saprotrophs and symbiotrophs proliferating under corn. Soil phosphorus (P) varied significantly by crop sequence, with lower levels of P corresponding with relative abundance of Glomerales, Paraglomerales, and Sebacinales and higher levels of P corresponding with relative abundance of Mortierellales. Soil density of the SCN was positively correlated with relative abundance and diversity of nematode-trapping fungi and with relative abundance of many potential nematode egg parasites. These results suggest several possible explanations for the improved yields associated with crop rotation, including decreased pathogen pressure, modification of soil properties, and increased diversity of soil fungal communities. Future research should investigate the potential of nematode-trapping fungi to regulate SCN densities and examine the relationships between soil P and specific arbuscular mycorrhizal and mortierellalean fungi associated with corn and soybean hosts.
Effects of α-tubulin acetylation on microtubule structure and stability
Authors: Eshun-Wilson Lisa , Zhang Rui , Portran Didier , Nachury Maxence , Toso Dan , Lohr Thomas , Vendruscolo Michele , Bonomi Massimiliano , Fraser James S. , Nogales Eva
Published: January 2019

Acetylation of K40 in α-tubulin is the sole post-translational modification to mark the luminal surface of microtubules. It is still controversial whether its relationship with microtubule stabilization is correlative or causative. We have obtained high-resolution cryo-electron microscopy reconstructions of pure samples of αTAT1-acetylated and SIRT2-deacetylated microtubules to visualize the structural consequences of this modification and reveal its potential for influencing the larger assembly properties of microtubules. We modeled the conformational ensembles of the unmodified and acetylated states by using the experimental cryo-EM density as the structural restraint in molecular dynamics simulations. We found that acetylation alters the conformational landscape of the flexible loop that contains αK40. Modification of αK40 reduces the disorder of the loop and restricts the states that it samples. We propose that the change in conformational sampling that we describe, at a location very close to the lateral contacts site, is likely to affect microtubule stability and function.
Non-invasive characterization of human bone marrow by cell free messenger-RNA reveals response to growth factor stimulation and hematopoietic reconstitution after transplantation
Authors: Ibarra Arkaitz , Zhao Yue , Salathia Neeraj S. , Zhuang Jiali , Huang Vera , Acosta Alexander D. , Aballi Jonathan , Toden Shusuke , Karns Amy P. , Purnajo Intan , Parks Julianna R. , Guo Lucy , Mason James , Sigal Darren , Nova Tina S. , Quake Stephen R. , Nerenberg Michael
Published: January 2019

Circulating cell free mRNA (cf-mRNA) holds great promise as a non-invasive diagnostic biomarker. However, the biological origin of cf-mRNA is still not well understood, limiting the clinical applications of this technology. Here, we use the bone marrow (BM) and pharmacologic manipulation of its resident cells as a window to study the origin of cf-mRNA. Using NGS-based profiling, we show that cf-mRNA is enriched in transcripts derived from the BM compared to circulating cells. Further, BM ablation experiments followed by hematopoietic stem cell transplants in cancer patients show that cf-mRNA levels reflect the transcriptional activity of BM resident hematopoietic lineages during marrow reconstitution. Finally, by stimulating specific BM cell populations in vivo using growth factor therapeutics (i.e. EPO, G-CSF), we show that cf-mRNA reveals dynamic functional changes in growing cell types, suggesting that, unlike other cell-free nucleic acids, cf-mRNA is secreted from living cells, rather than exclusively from apoptotic cells. Our results shed new light on the biology of cf-mRNA and demonstrate its potential applications in clinical practice.
DYRK1A-related intellectual disability: a syndrome associated with congenital anomalies of the kidney and urinary tract
Authors: Blackburn Alexandria T.M. , Bekheirnia Nasim , C. Uma Vanessa , Rosenfeld Jill A. , Bainbridge Matthew N. , Yang Yaping , Liu Pengfei , Madan-Khetarpal Suneeta , Delgado Mauricio R. , Hudgins Louanne , Krantz Ian , Rodriguez-Buritica David , G. Wheeler Patricia , Gazali Lihadh Al , Mohamed Al Shamsi Aisha Mohamed Saeed , Gomez-Ospina Natalia , Chao Hsiao-Tuan , Mirzaa Ghayda M. , Scheuerle Angela E. , Kukolich Mary K , Scaglia Fernando , Eng Christine , Braun Michael C. , Lamb Dolores J. , Miller Rachel K. , Bekheirnia Mir Reza
Published: January 2019

Purpose

Haploinsufficiency of DYRK1A causes a recognizable clinical syndrome. The goal of this paper is to investigate congenital anomalies of the kidney and urinary tract (CAKUT) and genital defects (GD) in patients with DYRK1A mutations.

Methods

A large database of clinical exome sequencing (ES) was queried for de novo DYRK1A mutations and CAKUT/GD phenotypes were characterized. Xenopus laevis (frog) was chosen as a model organism to assess Dyrk1a’s role in renal development.

Results

Phenotypic details and mutations of 19 patients were compiled after an initial observation that one patient with a de novo pathogenic mutation in DYRK1A had GD. CAKUT/GD data were available from 15 patients, 11 of whom present with CAKUT/GD. Studies in Xenopus embryos demonstrate that knockdown of Dyrk1a disrupts the development of segments of developing embryonic nephrons, which ultimately give rise to the entire genitourinary (GU) tract. These defects could be rescued by co-injecting wildtype human DYRK1A RNA, but not with truncated DYRK1AR205* RNA.

Conclusion

Evidence supports routine GU screening of all individuals with de novo DYRK1A pathogenic variants to ensure optimized clinical management. Collectively, the reported clinical data and loss of function studies in Xenopus substantiate a novel role for DYRK1A in GU development.
Evolutionary Dynamics Do Not Motivate a Single-Mutant Theory of Human Language
Authors: de Boer Bart , Thompson Bill , Ravignani Andrea , Boeckx Cedric
Published: January 2019

One of the most controversial hypotheses in cognitive science is the Chomskyan evolutionary conjecture that language arose instantaneously in our species as the result of a single staggeringly fortuitous mutation. Here we analyze the evolutionary dynamics implied by this hypothesis, which has never been formalized. The theory supposes the emergence and fixation of a single mutant (capable of the syntactic operationMerge) during a narrow historical window as a result of frequency-independent selection under a huge fitness advantage in a population of an effective size that is standardly assumed to have been no larger than ~15 000 early humans. We examine this proposal by combining diffusion analysis and extreme value theory to derive a probabilistic formulation of its dynamics. Perhaps counter-intuitively, a macro-mutation is much more unlikelya priorithan multiple mutations with smaller fitness effects, yet both hypotheses predict fixation with high conditional probability. The consequences of this asymmetry have not been accounted for previously. Our results diffuse any suggestion that evolutionary reasoning provides an independent rationale for the controversial single-mutant theory of language.

Significance statement

In recent years, Chomsky and colleagues have sought support for their minimalist theory of the language faculty from evolutionary considerations. They have argued for a spontaneous emergence of a mutation conferring an advantage for thought independent of communication. Here for the first time a formalization of this view is offered, and contrasted with a more gradual evolutionary scenario. The outcome of our analysis argues against the Chomskyan view.