bluuebunny/crossref_metadata_2025 huggingface dataset:
The reflexive imperative among high-achieving adolescents
Authors: Van Lancker Inge
Published: January 2017

The socio-cultural conditions of late modernity induce a “reflexive imperative” amongst young people, which also results in metapragmatic and metalinguistic behaviour, as has been demonstrated by linguistic ethnographers (LE). However, recent LE studies on reflexivity in Western European settings have mainly focused on how groups of socially low-status, geographically mobile and multilingual youth are involved in creative linguistic processes in which the disapproval of their linguistic hybridity is denounced. In this paper, based on a linguistic-ethnographic study, I will uncover the influence of the reflexive imperative on a different group: six high-achieving, white, elite, male, adolescent pupils in Flemish Belgium. Through a micro-analysis of their metacommentaries and speech practices, I describe the subtle metalinguistic and metapragmatic moves of the pupils, which demonstrate their attitude towards standard language use at school. An analysis of these boys’ linguistic reflexivity demonstrates a complex attitude towards Standard Dutch and Standard Language Ideology: at first sight, they seem to incline towards linguistic equality, resulting in a relaxation of the standard norm. However, an analysis of the more indirect metapragmatic practices of these boys reveals how they strategically use the symbolic capital of Standard Dutch, a practice which echoes the Flemish language-in-education policy and might serve to preserve (or prepare) their (future) elite position in society.
Reflexivity and transnational habitus
Authors: De Costa Peter I. , Tigchelaar Magda , Cui Yaqiong
Published: January 2017

Following Sayer’s (2010) examination of reflexivity and habitus, we focus on the transnational habitus (Darvin
& Norton 2015) of Aaron, a Chinese international student at a U.S. university. Specifically, we examine how he wrestled with
being identified as an ESL learner despite having attended a U.S. high school. Also exploring the relationship between reflexivity
and emotions (Flam 2010), we draw on his written work, interviews, and his WeChat conversations. Our findings revealed that as a
result of positioning himself as being better than the other Chinese students on campus (because of his English proficiency) and
distancing himself from domestic U.S. students, Aaron did not capitalize on his Chinese-English bilingualism to extend his local
social networks, which exacerbated his growing isolation at his home university. In tracing his emotional trajectory and
strategies to cope with his predicament, we problematize the grand narrative of the global elite (Vandrick 2011)
that overlooks the challenges encountered by affluent international students.
Effects of different teaching methods on the production of Mandarin tone 3 by English speaking learners
Authors: He Yunjuan , Wang Qian , Wayland Ratree
Published: January 2017

This study compared the effectiveness of two teaching methods on the production of Mandarin Tone 3 by English-speaking students. The control group (n=12) received pitch direction-focused instruction in which Tone 3 was introduced as a falling-rising contour tone while the experimental group (n=12) received pitch height-focused instruction in which Tone 3 was introduced as a low level tone. The ability to produce this tone in monosyllabic words, disyllabic words and sentences was assessed after 1 month, 2 months, and 3 months of instruction. The results showed that the pitch height-focused teaching method improved Tone 3 production in connected tonal environments at the sentence level, whereas the pitch direction-focused teaching method was more effective in training students to produce this tone in isolation. More importantly, unlike the pitch direction-focused method, the effectiveness of the pitch height-focused teaching method generalized to new words. It helped L2 learners to develop a self-learning skill for pronouncing unfamiliar words.
The discourses of the Greek crisis
Authors: Hatzidaki Ourania , Goutsos Dionysis
Published: January 2017

The introduction to the volume offers an overview of existing research on the discourse pertaining to the Greek crisis and relates this to the papers included in it. It is suggested that previous works mainly focused on how the Greek crisis has been communicated by the mass media, and viewed from abroad. By contrast, this volume looks at how the Greeks themselves construe their own predicament, investigating a rich diversity of local voices, elite, non-elite and resistance. Methodologically, contrary to extant research, which principally draws on the results of content analysis, this volume concentrates on the mechanics of Greek crisis rhetoric. To this end, papers combine a sizeable array of corpus linguistics and critical discourse analysis techniques, employed in multifarious ways so as to provide nuanced analyses of Greek crisis discourses.
The dream that turned into a nightmare
Authors: Kostopoulou Georgia
Published: January 2017

This study aims at shedding light on the evolution of the pre-electoral discourse of two of the most prominent politicians of the 2000s, centre right-wing Kostas Karamanlis and social-democrat George Papandreou and, in particular, on the transformation of their lexical choices across three pre-crisis national election campaigns (2004, 2007 and 2009). Furthermore, it critically presents lexical choices with positive and negative prosody for the voting audience and examines how they function as rhetorical tools for persuading and manipulating the addressees (traditional, potential and swing voters) in the light of the broader socio-political context.
The “theory of the two extremes”
Authors: Hatzidaki Ourania
Published: January 2017

This chapter reports on a large-scale quantitative and qualitative investigation of the use of the notion of “extremism” in the public discourse of significant political actors during the Greek crisis. It focuses on its employment as a rhetorical tool for the stigmatization of political opponents, specifically for the delegitimation, by the government representatives at the time (New Democracy and PASOK), of potentially threatening political/electoral rivals (principally SYRIZA and the Left, and secondarily Golden Dawn). We also examine the reaction of the stigmatized, by analysing the discourse of the parliamentary opposition, extra-parliamentary web fora and social-revolutionary terrorists, where several strategies of response are identified. We observe that respondents universally prefer lower-key rhetorical techniques, probably in an effort to disconfirm the politically costly extremism reproach.
“Tragic event” vs. “cowardly murder”
Authors: Fragaki Georgia
Published: January 2017

This chapter discusses the representation, in texts published on the Golden Dawn official website, of Pavlos Fyssas’ murder by a Golden Dawn member and the subsequent murders of two members of this party by as yet unidentified perpetrators. The diachronically-sensitive analysis of keywords, clusters and concordances relating to processes and participants suggests that the discourse treatment of the two cases differs fundamentally: lexicogrammatical choices position the two incidents at removed points on a detachment vs. involvement scale, and also reveal significantly different levels of interest in the actor(s) and abettors associated with each incident. The discourse strategies identified in the texts (e.g. denial, variously downtoning or foregrounding of events, counterattack by reversal of accusations) concur with these choices and allow Golden Dawn to appear as a victim (victim-victimizer reversal).
Golden Dawn and the traits of extreme right-wing discourse amidst the Greek crisis
Authors: Saridakis Ioannis E.
Published: January 2017

This is a corpus-driven study of the lexical and textual semantics and pragmatics of Greek neo-nationalist discourse at the time of the Greek crisis. A corpus of texts culled from Golden Dawn’s website has been examined by corpus linguistics and critical discourse analysis techniques in order to investigate the positioning of Greek neo-nationalist discourse and identify the conceptual link between the rampant crisis and the ideology of this extreme-right party. The focus is on the lexical and argumentative means used by Golden Dawn to formulate its core ideological pillars by exploiting the crisis and to establish itself in the political and social arena.
Scope and partitivity of plural indefinite noun phrases in Spanish
Authors: Colomina-Almiñana Juan J.
Published: January 2017

It has been argued that European Spanish plural indefinite noun phrases includingalgunosconvey a partitive effect because the restrictoralg-provides additional properties. The reason thatalgunosimplicates a “non-all-things” effect is because it refers only to an indeterminate part of the whole. The scope of bare plurals andunos, in contrast, does not exhibit this characteristic. This article argues that, contrarily to this claim, the scope of bare plurals andunosalso induces partitivity because occurrences of these words include unarticulated constituents. Therefore, European Spanish indefinite noun phrases pragmatically presuppose the relevant part of what the speaker intends to refer, which is also shared by the audience since it is part of the common ground both occupy. Hence, bare plurals andunosare always contextually restricted, since a covert (optional) variable present in the logical form cannot capture this contextual restriction.
Aligning caller and call-taker
Authors: Koole Tom , Verberg Nina
Published: January 2017

This paper reports on conversation analytic research for the Dutch national emergency call-centre. In a corpus study of 120 emergency calls we show that callers’ orientations to their communicative tasks are not aligned to the institutional communicative tasks of the call-takers. In a subsequent workplace experiment involving over 2000 calls, it appeared that the use of an alternative question rather than a wh-question, significantly altered callers’ emergency deliveries and adapted them to call-takers’ communicative needs. The analysis shows two aspects of callers’ responses to the different question formats: (i) The alternative questions produced significantly more type-conforming answers than the wh-questions, and also (ii) callers treated their non-conforming answer to alternative question more often as dispreferred than their non-conforming answers to wh-questions. Callers thus treated the preference for type-conformity to be stronger for alternative questions than for wh-questions.
The hypothesis of insubordination and three types of wh-exclamatives
Authors: Zevakhina Natalia
Published: January 2017

This paper provides evidence for Evans’ (2007) insubordination hypothesis w.r.t. wh-exclamatives. It investigates word order in matrix wh-exclamatives and their subordinate correlates and tests matrix-subordinate asymmetry (the felicitousness of wh-words in matrix and subordinate contexts). It establishes distinctions among three groups of wh-exclamatives. Group 1 comprises qualitative and quantitative wh-exclamatives, which together seem to be a basic cross-linguistic wh-exclamative pattern. The qualitative variety demonstrates several strategies of using wh-words, some of which are exclamative-only and/or are sensitive to ellipsis of a gradable adjective/adverb. Group 2 implies the semantic hierarchy w.r.t. the felicitousness of wh-words in matrix exclamatives: ‘what’/‘who’/‘where’>‘when’>‘why’. Group 3 includes ‘which’, ‘what kind’, ‘how’ (manner) exclamatives. Unlike Groups 1 and 3, Group 2 is subject to cross-linguistic variation w.r.t. matrix-subordinate asymmetry. The paper suggests partial overlap between the established classification of wh-exclamatives and the classification developed by Nouwen and Chernilovskaya (2015) and has implications for an exclamative sentence type.
Agent-defocusing constructions from nominalized VPs
Authors: Sansò Andrea
Published: January 2017

Nominalized verb phrases have been identified as a possible source of passive and impersonal constructions by Langacker & Munro (1975), Langacker (1976), and Givón (1981), with exemplification drawn almost exclusively from Uto-Aztecan languages, but have received relatively less attention than other sources (reflexive markers, generalized subject constructions, 3rd person plural constructions, inactive auxiliaries + resultative participles, etc.). The aim of this article is to review the available evidence concerning passive and impersonal constructions derived from nominalized VPs, with a view to establishing whether they are cross-linguistically recurrent and robust as a type. Such a review reveals that there are overall a few instances of passive/impersonal constructions that are likely to derive from nominalized VPs. In many of the other cases in which a nominalized VP has been hypothesized to be the source of a given passive or impersonal construction there is no conclusive evidence for reconstructing such a source, and in some cases even an alternative source can be posited. Even in this unfavourable situation, however, a tentative scenario of how nominalized VPs might evolve into passive and impersonal constructions may be sketched, in order to account for the few cases in which such a development is likely to have taken place. The onset stage of this development, in particular, capitalizes on the possibility offered by nominalized VPs to manipulate the argument structure of the verb by keeping the initiator of the event off the stage.
Subject pronoun doubling in Agul
Authors: Maisak Timur A.
Published: January 2017

The paper describes the doubling of free personal pronouns in Agul, an East Caucasian language spoken in Daghestan, Russia. The doubling construction consists of a subject pronoun in the canonical preverbal position, paired with an identical instance of the same pronoun immediately following the verb. The first pronoun is usually adjacent to the “verb–pronoun” combination, though it can optionally be separated by another constituent. In the oral corpus consulted for the analysis, the construction is found most often with the primary verb of speech in clauses introducing a quote (e.g. ‘I said I, …’). I argue that the doubling pattern originated as the conflation of a preverbal subject with a very frequent “verb–subject” word order used with highly topical referents. The function of the doubling construction is therefore postulated to draw additional attention to the referent. A brief comparison of Agul doubling and related phenomena in other languages (e.g. person agreement and clitic doubling) is also offered.
Modelling of recalescence effect on austenite decomposition
Authors: Guo Lei , Roelofs Hans , Lembke Mirkka Ingrid , Bhadeshia Harshad Kumar Dharamshi Hansraj
Published: January 2017

A model for recalescence has been established by integrating a model for the decomposition of austenite and one dealing with heat transfer with latent heat release taken into account. The effects of recalescence on each individual austenite transformation product have been studied. It was found that Widmanstätten ferrite and pearlite reactions are most affected. The calculated cooling curve, as affected by the recalescence, has also been verified with a commercial steel subjected to two different environment conditions.
Ti and nitride surface modification of copper by pack cementation
Authors: Stathokostopoulos D. , Chaliampalias D. , Pliatsikas N. , Kassavetis S. , Pavlidou E. , Patsalas P. , Logothetidis S. , Chrissafis K. , Vourlias G.
Published: January 2017

Copper is widely applied however its disadvantages such as low hardness and poor oxidation resistance. TiN coatings are often used industrially for overriding such disadvantages of ferrous components. In this examination the deposition of TiN on Cu substrates is investigated for the first time by pack cementation process with which one or more elements can be deposited simultaneously by gas and solid-state diffusion reactions. This feature makes this process very attractive for industrial use as it is economic and time saving. Microstructural examination of the deposited samples revealed the formation of thick coatings corresponding to Ti–Cu phases. Focusing on the coating surface it was found that a TiN thin layer is formed. This was verified also from hardness measurements which showed that there was a significant increase of the surface hardness. Furthermore, the oxidation resistance of the coated samples has considerably increased as implied from the thermogravimetric measurements.
Investigation of pulse electrodeposited Ni–Co/SiO2 nanocomposite coating
Authors: Ghazanlou S. I. , Ahmadiyeh S. , Yavari R.
Published: January 2017

Ni–Co/SiO2 nanocomposite coating was deposited on the steel substrate by pulse electrodeposition method. The coatings were characterised by X-ray diffraction, field emission scanning electron microscopy technique, energy-dispersive X-ray spectroscopy and X-ray map (dispersive elemental mapping) analysis. The influences of stirring rate, pH and SiO2 concentration parameters on the mechanical properties and corrosion resistance were studied. The zeta potential of SiO2 nanoparticles was decreased by mounting the pH and also adsorption of the surfactant SDS. Microhardness, friction coefficient, wear and anodic polarisation were determined through Buhler microhardness tester, pin-on-disc wear test and potentiostat galvanic device, respectively. By applying optimum electrodeposition condition (stirring rate 200 rev min−1, pH 4.6 and SiO2 concentration 20 gL−1) incorporation of SiO2 particles into the nickel–cobalt matrix increases which results in the preparation of coatings with high microhardness and corrosion resistance, low friction coefficient and wear mass loss.
Influence of coating thickness on the morphology of TiC particles
Authors: Cai Yangchuan , Luo Zhen , Chen Yao , Ma Chengyong , Song Renfeng
Published: January 2017

The TiC/Al-based composite coatings with different thickness were fabricated on the AZ31B magnesium alloy by laser cladding. The distribution of TiC ceramic particles in the cladding layers was not uniform, and the reunion degree increased with the increase of cladding layer thickness. The cladding layers mainly contained Al, γ-Al12Mg17, β-Al3Mg2, and TiC phases. γ-Al12Mg17 mainly distributed in the bottom of the cladding layers, and β-Al3Mg2 distributed in the middle and surface zones. The contents of γ-Al12Mg17 and β-Al3Mg2 have the inverse proportion to the thickness of the cladding layers, and the TiC content is irregular. The micro-hardness value was increased with the increase of the cladding layers thickness, and the thicker the cladding layers, the greater the fluctuations of the micro-hardness. The wear resistance of the cladding layer had the positive proportion to the hardness. TiC ceramic particles could cause the exfoliation in the wear test.
Tribological performances of textured surfaces prepared by electrodeposition method
Authors: Liu Derong , Wu Zhong , Yan Bo , Shen Bin , Liu Lei , Hu Wenbin
Published: January 2017

Surface texturing has become an increasingly prevalent approach to improve tribological properties of materials. In this work, textured surfaces, fabricated by means of electrodeposition, were studied by measuring the tribological properties. An improved method relying on material ratio curve was used to obtain more accurate wear volumes for the textured surfaces. The results showed that the bumps are distributed on the surfaces in a random array. Compared with the untextured surface, textured surfaces show lower friction and significantly improved wear resistance. The troughs around the bumps act as pockets for collecting the abrasive particles, which minimise the friction and wear of surfaces.
Building tribal communities in the collaborative economy: an innovation framework
Authors: Barnes Stuart J. , Mattsson Jan
Published: January 2017

In recent years, there has been a groundswell of initiatives aimed at providing platforms to share resources among people. Collaborative consumption provides a model for a ‘sharing economy’ where the dominant logic of consumers is resource access rather than ownership. This study examines the nature and development of a variety of collaborative consumption businesses; in particular, we explore how start-up entrepreneurs see the problems of creating a tribal community among customers and users. Interviews were carried out with founders and co-founders of collaborative consumption ventures during 2014–15. The results suggest that these organisations face many common issues. We develop and apply a framework to understand some of these. We find that collaborative consumption entrepreneurs strive to build a tribal community by matching, in an innovative way, supply and demand. This is typically done by co-creating shared commonality, developing scalable electronic platforms, and building trust into platforms using social media to develop proxy social capital. Consequently, by using existing ecosystems of social media, tribal communities can be formed and scaled much more quickly than via traditional marketing approaches.
Many roads to symmetry breaking: molecular mechanisms and theoretical models of yeast cell polarity
Authors: Goryachev Andrew B. , Leda Marcin
Published: January 2017

Mathematical modeling has been instrumental in identifying common principles of cell polarity across diverse systems. These principles include positive feedback loops that are required to destabilize a spatially uniform state of the cell. The conserved small G-protein Cdc42 is a master regulator of eukaryotic cellular polarization. Here we discuss recent developments in studies of Cdc42 polarization in budding and fission yeasts and demonstrate that models describing symmetry-breaking polarization can be classified into six minimal classes based on the structure of positive feedback loops that activate and localize Cdc42. Owing to their generic system-independent nature, these model classes are also likely to be relevant for the G-protein–based symmetry-breaking systems of higher eukaryotes. We review experimental evidence pro et contra different theoretically plausible models and conclude that several parallel and non–mutually exclusive mechanisms are likely involved in cellular polarization of yeasts. This potential redundancy needs to be taken into consideration when interpreting the results of recent cell-rewiring studies.
How does social support affect functional impairment in late life? Findings of a multicenter prospective cohort study in Germany
Authors: Hajek André , Brettschneider Christian , Mallon Tina , van der Leeden Carolin , Mamone Silke , Wiese Birgitt , Weyerer Siegfried , Werle Jochen , Fuchs Angela , Pentzek Michael , Riedel-Heller Steffi G. , Stein Janine , Bickel Horst , Weeg Dagmar , Heser Kathrin , Wagner Michael , Maier Wolfgang , Scherer Martin , Luck Tobias , König Hans-Helmut
Published: January 2017

Objective

to investigate how social support affects functional impairment (FI) in late life in a longitudinal approach.

Methods

in a multicenter prospective cohort study, subjects in old age (≥75 years at baseline) were interviewed every 1.5 years. Social support was quantified in the follow-up (FU) Waves 2 and 4 (FU Wave 2: n = 2,349; FU Wave 4: n = 1,484). FI was assessed by using the Lawton and Brody Instrumental Activities of Daily Living scale.

Results

fixed effects regressions showed that a decrease in social support is associated with FI in the total sample and in both sexes. The effect on FI was most pronounced with the dimension social integration, whereas changes in practical support only affected FI in the total sample and changes in emotional support only affected FI in men.

Conclusions

our findings emphasise the importance of social support for functional status in late life. Thus, strengthening social support in old age might be effective in maintaining functional abilities.
Soda Taxes and the Prices of Sodas and Other Drinks: Evidence from Mexico
Authors: Grogger Jeffrey
Published: January 2017

To combat a growing obesity problem, Mexico imposed a nationwide tax on drinks with added sugar, popularly referred to as a “soda tax,” effective January 2014. Since the tax took effect nationwide, there is no conventional control group that can be used as a baseline to estimate how the tax affected prices. Instead, I make use of control commodities, that is, untaxed goods that are not substitutes for the taxed drinks. I analyze data from Mexico's Consumer Price Index program, using the synthetic control method and a time‐series intervention analysis. In both cases I employ a placebo inference approach akin to permutation inference. The estimates show that soda prices rose by more than the amount of the tax. There is less evidence that the prices of potential substitutes rose, possibly indicating that consumers did not switch to those products after the tax took effect. Some simple calculations suggest that the soda price increase could lead to a two‐ to three‐pound reduction in mean weight, which amounts to roughly 1%–2% of mean body mass.
High-Salt Intake Augments the Activity of the RhoA/ROCK Pathway and Reduces Intracellular Calcium in Arteries From Rats
Authors: Crestani Sandra , Webb Robert Clinton , da Silva-Santos José Eduardo
Published: January 2017

BACKGROUND

We investigated the influence of salt overconsumption on the functionality of the RhoA/Rho-associated kinase (ROCK) pathway and calcium regulation in arteries.

METHODS

The aorta and small mesenteric arteries from rats fed a chow containing 2%, 4%, or 8% NaCl were evaluated in organ baths for the activity of the RhoA/ROCK pathway and intracellular calcium mobilization. Components of these pathways and intracellular calcium levels were also assessed in samples from 4% NaCl group.

RESULTS

In arteries from animals fed regular chow, the ROCK inhibitor Y-27632 reduced the responses to phenylephrine, even when the smallest concentrations (1 and 3 μM) were tested. However, only higher concentrations of Y-27632 (10 and 50 μM) reduced phenylephrine-induced contraction in vessels from high-salt groups. Immunoblotting revealed augmented phosphorylation of the myosin phosphatase targeting subunit 1 and increased amounts of RhoA in the membrane fraction of aorta homogenates from the 4% NaCl group. Under calcium-free solution, vessels from NaCl groups presented reduced contractile responses to phenylephrine and caffeine, compared with the regular chow group. Moreover, decreased intracellular calcium at rest and after stimulation with ATP were found in aortic smooth muscle cells from 4% NaCl-fed rats, which also showed diminished levels of SERCA2 and SERCA3, but not of IP3 and ryanodine receptors, or STIM1 and Orai1 proteins.

CONCLUSIONS

Arteries from rats subjected to high-salt intake are unable to properly regulate intracellular calcium levels and present augmented activity of the calcium sensitization pathway RhoA/ROCK. These changes may precede the development of vascular diseases induced by high-salt intake.
Predictive Significance of Day-to-Day Blood Pressure Variability in Acute Ischemic Stroke for 12-Month Functional Outcomes
Authors: Shi Zhu , Li En S. , Zhong Jun S. , Yuan Juan L. , Li Lan R. , Zheng Cheng W.
Published: January 2017

BACKGROUND

Previous studies on the association between blood pressure (BP) variability in acute ischemic stroke and functional outcomes have yielded conflicting results. We aimed to investigate the predictive significance of day-to-day BP variability during the 7 days following stroke onset for functional outcomes at 12 months.

METHODS

A total of 229 patients (male 68.8%, mean age 66.7 ± 13.0 years) within 24 hours after onset were prospectively studied. The first 24 hours and day-to-day BP variability, including the SD, coefficient variation (CV), average real variation, and ΔBP (difference between the maximum and minimum BP), were derived and compared to functional outcomes. The functional outcomes were accessed using the baseline severity-adjusted analysis at 12 months post-stroke.

RESULTS

The patients with poor outcomes at 12 months had significantly higher morning systolic BP (SBP; 1–3 days after onset) than those with good outcomes. The day-to-day SBP variability parameters (1–7 days) such as SD, CV, and Δ SBP were significantly higher in the patients with poor outcomes than in those with good outcomes (17.0 ± 6.0 vs. 14.8 ± 5.3 mm Hg, 11.8 ± 3.9 vs. 10.6 ± 3.5, 48.3 ± 17.7 vs. 39.9 ± 15.5 mm Hg, respectively; P < 0.05). After adjustment for demographic and clinical features, day-to-day Δ SBP was associated with poorer functional outcomes at 12 months (odds ratio, 95% confidence interval: 1.547, 1.097–2.181). Even after adjusting for the mean SBP, Δ SBP was independently associated with 12-month poor functional outcomes (odds ratio, 95% confidence interval: 1.577, 1.095–2.272).

CONCLUSIONS

Day-to-day SBP variability in acute ischemic stroke was associated with poor functional outcomes at 12 months.

CLINICAL TRIALS REGISTRATION

Trial Number NCT02675972
Hypertension and Atrial Fibrillation: An Intimate Association of Epidemiology, Pathophysiology, and Outcomes
Authors: Dzeshka Mikhail S. , Shahid Farhan , Shantsila Alena , Lip Gregory Y.H.
Published: January 2017

Atrial fibrillation (AF) is the most prevalent sustained arrhythmia found in clinical practice. AF rarely exists as a single entity but rather as part of a diverse clinical spectrum of cardiovascular diseases, related to structural and electrical remodeling within the left atrium, leading to AF onset, perpetuation, and progression. Due to the high overall prevalence within the AF population arterial hypertension plays a significant role in the pathogenesis of AF and its complications. Fibroblast proliferation, apoptosis of cardiomyocytes, gap junction remodeling, accumulation of collagen both in atrial and ventricular myocardium all accompany ageing-related structural remodeling with impact on electrical activity. The presence of hypertension also stimulates oxidative stress, systemic inflammation, rennin–angiotensin–aldosterone and sympathetic activation, which further drives the remodeling process in AF. Importantly, both hypertension and AF independently increase the risk of cardiovascular and cerebrovascular events, e.g., stroke and myocardial infarction. Given that both AF and hypertension often present with limited on patient wellbeing, treatment may be delayed resulting in development of complications as the first clinical manifestation of the disease. Antithrombotic prevention in AF combined with strict blood pressure control is of primary importance, since stroke risk and bleeding risk are both greater with underlying hypertension.
Cigarette Smoking and Subtypes of Uncontrolled Blood Pressure Among Diagnosed Hypertensive Patients: Paradoxical Associations and Implications
Authors: Liu Xuefeng , Byrd James Brian
Published: January 2017

BACKGROUND

Isolated uncontrolled systolic blood pressure (SBP), uncontrolled systolic-diastolic blood pressure (BP), and isolated uncontrolled diastolic blood pressure (DBP) are subtypes of uncontrolled BP. The associations of smoking with uncontrolled BP subtypes among diagnosed hypertensive patients are unknown.

METHODS

Seven thousand eight hundred twenty-nine subjects aged 18 years or over with diagnosed hypertension were selected from the National Health and Nutrition Examination Survey with stratified multistage clustered sampling design. Weighted logistic regressions were conducted to estimate odds ratios (ORs) with 95% confidence intervals (CIs) of uncontrolled BP subtypes related to smoking status. Weighted multiple regression models were used to examine the association of smoking with levels of SBP, DBP, and pulse pressure.

RESULTS

The average age of the study sample was 60.3 ± 0.3 years. 54.2% ± 0.7% were females. Compared to nonsmokers, current smokers were 22% less likely to have uncontrolled BP (OR: 0.78, 95% CI: 0.64–0.94, P = 0.01), and 21% less likely to have isolated uncontrolled SBP (OR: 0.79, 95% CI: 0.64–0.97, P = 0.02). Average DBP was 1.5 mm Hg lower (95% CI: −2.8 to −0.2 mm Hg, P = 0.02) in current smokers than in nonsmokers. Average DBP was 0.9 mm Hg lower (95% CI: −1.7 to −0.03 mm Hg, P = 0.04) in former smokers than in nonsmokers. Current smoking and former smoking were not associated with risk of uncontrolled systolic–diastolic BP and isolated uncontrolled DBP.

CONCLUSIONS

Paradoxical associations between current smoking and SBP, uncontrolled BP and isolated uncontrolled SBP were shown among hypertensive patients. The explanation for these associations is currently unknown. No cause–effect relationships should be assumed.
Blood Pressure Control During Chronic Kidney Disease Progression
Authors: Lee Seulbi , Oh Hyung Jung , Lee Eun-Kyung , Lee Oesook , Ha Eunhee , Kim Seung-Jung , Kang Duk-Hee , Choi Kyu Bok , Ryu Dong-Ryeol
Published: January 2017

BACKGROUND

Hypertension is a major cause of end-stage renal disease, and blood pressure (BP) control is crucial in patients with chronic kidney disease (CKD). However, it is generally inadequately controlled in CKD patients. We investigated the prevalence of CKD patients with inadequate BP control and its related factors, based on the CKD stage.

METHODS

We analyzed the health examination sample cohort database, which consisted of the randomly selected participants among all the citizens who received the health examination provided by National Health Insurance Service of Korea in 2012 and 2013.

RESULTS

There were 27,350 CKD patients (7.9%) out of a total of 345,044 participants. As CKD stage progressed, there were more patients with poorly controlled hypertension compared to those with well-controlled hypertension. In addition, systolic BP increased with CKD stage progression, while diastolic BP was not significantly different. Age, female, body mass index, increased pulse pressure, CKD stage, and levels of fasting glucose, total cholesterol, hemoglobin, and proteinuria were significant factors associated with poor control of BP in hypertensive CKD patients.

CONCLUSION

The proportion of CKD patients with poorly controlled hypertension significantly increased as CKD progressed, mainly associated with the increase in pulse pressure. However, future investigation for causal relationship between poorly controlled hypertension and its related factors is needed.
The Effects of Trivialization of Workplace Violence on Its Victims: Profession and Sex Differences in a Cross-Sectional Study among Healthcare and Law Enforcement Workers
Authors: Geoffrion Steve , Goncalves Jane , Boyer Richard , Marchand André , Guay Stéphane
Published: January 2017

Background:

Workers from the law enforcement and healthcare sectors tend to normalize or mute their victimization from workplace violence (WPV).

Objectives:

This study aims to assess the impact of the trivialization of WPV on psychological consequences for workers who have been affected by a WPV incident. The second aim is to assess the moderating effect of sex on the trivialization of WPV. The third and overarching aim is to assess the moderating effect of professional identity on the relations between individual and organizational factors and psychological consequences following a WPV incident.

Methods:

The findings are based on a convenience sample of 377 (204 female and 173 male) workers from the law enforcement and healthcare sectors. Individual factors (sex, age, professional identity, prior victimization, witnessing WPV, injuries, and trivialization of violence) and perceived support factors (colleagues’ support and employer’s support) were used as predictor variables of psychological consequences in hierarchical linear regression models. Sex was used as a moderator of trivialization while professional identity was used as a moderator of all predictors.

Findings:

When individual and social support factors were controlled for, normalizing violence was negatively associated with psychological consequences while perceiving a taboo associated with complaining about WPV was positively associated for all participants. When these relations were moderated by the sex of the participants and then by their professional identity, normalization was found to decrease psychological consequences only for male healthcare workers.

Implications:

To help employees cope with WPV, organizations should promote strategies adapted to profession and sex differences. For male healthcare workers, normalization as a cognitive coping strategy should be formally recognized. For both professions and sexes, organizational strategies that counter the perceived taboo of complaining about violence should be reinforced.
Sparse network modeling and metscape-based visualization methods for the analysis of large-scale metabolomics data
Authors: Basu Sumanta , Duren William , Evans Charles R , Burant Charles F , Michailidis George , Karnovsky Alla
Published: January 2017

Motivation

Recent technological advances in mass spectrometry, development of richer mass spectral libraries and data processing tools have enabled large scale metabolic profiling. Biological interpretation of metabolomics studies heavily relies on knowledge-based tools that contain information about metabolic pathways. Incomplete coverage of different areas of metabolism and lack of information about non-canonical connections between metabolites limits the scope of applications of such tools. Furthermore, the presence of a large number of unknown features, which cannot be readily identified, but nonetheless can represent bona fide compounds, also considerably complicates biological interpretation of the data.

Results

Leveraging recent developments in the statistical analysis of high-dimensional data, we developed a new Debiased Sparse Partial Correlation algorithm (DSPC) for estimating partial correlation networks and implemented it as a Java-based CorrelationCalculator program. We also introduce a new version of our previously developed tool Metscape that enables building and visualization of correlation networks. We demonstrate the utility of these tools by constructing biologically relevant networks and in aiding identification of unknown compounds.

Availability and Implementation

http://metscape.med.umich.edu

Supplementary information

Supplementary data are available at Bioinformatics online.
Genotyping inversions and tandem duplications
Authors: Ebler Jana , Schönhuth Alexander , Marschall Tobias
Published: January 2017

Motivation

Next Generation Sequencing (NGS) has enabled studying structural genomic variants (SVs) such as duplications and inversions in large cohorts. SVs have been shown to play important roles in multiple diseases, including cancer. As costs for NGS continue to decline and variant databases become ever more complete, the relevance of genotyping also SVs from NGS data increases steadily, which is in stark contrast to the lack of tools to do so.

Results

We introduce a novel statistical approach, called DIGTYPER (Duplication and Inversion GenoTYPER), which computes genotype likelihoods for a given inversion or duplication and reports the maximum likelihood genotype. In contrast to purely coverage-based approaches, DIGTYPER uses breakpoint-spanning read pairs as well as split alignments for genotyping, enabling typing also of small events. We tested our approach on simulated and on real data and compared the genotype predictions to those made by DELLY, which discovers SVs and computes genotypes, and SVTyper, a genotyping program used to genotype variants detected by LUMPY. DIGTYPER compares favorable especially for duplications (of all lengths) and for shorter inversions (up to 300 bp). In contrast to DELLY, our approach can genotype SVs from data bases without having to rediscover them.

Availability and Implementation

https://bitbucket.org/jana_ebler/digtyper.git.

Supplementary information

Supplementary data are available at Bioinformatics online.
PALADIN: protein alignment for functional profiling whole metagenome shotgun data
Authors: Westbrook Anthony , Ramsdell Jordan , Schuelke Taruna , Normington Louisa , Bergeron R Daniel , Thomas W Kelley , MacManes Matthew D
Published: January 2017

Motivation

Whole metagenome shotgun sequencing is a powerful approach for assaying the functional potential of microbial communities. We currently lack tools that efficiently and accurately align DNA reads against protein references, the technique necessary for constructing a functional profile. Here, we present PALADIN—a novel modification of the Burrows-Wheeler Aligner that provides accurate alignment, robust reporting capabilities and orders-of-magnitude improved efficiency by directly mapping in protein space.

Results

We compared the accuracy and efficiency of PALADIN against existing tools that employ nucleotide or protein alignment algorithms. Using simulated reads, PALADIN consistently outperformed the popular DNA read mappers BWA and NovoAlign in detected proteins, percentage of reads mapped and ontological similarity. We also compared PALADIN against four existing protein alignment tools: BLASTX, RAPSearch2, DIAMOND and Lambda, using empirically obtained reads. PALADIN yielded results seven times faster than the best performing alternative, DIAMOND and nearly 8000 times faster than BLASTX. PALADIN's accuracy was comparable to all tested solutions.

Availability and Implementation

PALADIN was implemented in C, and its source code and documentation are available at https://github.com/twestbrookunh/paladin

Supplementary information

Supplementary data are available at Bioinformatics online.
Supporting precision medicine by data mining across multi-disciplines: an integrative approach for generating comprehensive linkages between single nucleotide variants (SNVs) and drug-binding sites
Authors: Roy Choudhury Amrita , Cheng Tiejun , Phan Lon , Bryant Stephen H , Wang Yanli
Published: January 2017

Motivation

Genetic variants in drug targets and metabolizing enzymes often have important functional implications, including altering the efficacy and toxicity of drugs. Identifying single nucleotide variants (SNVs) that contribute to differences in drug response and understanding their underlying mechanisms are fundamental to successful implementation of the precision medicine model. This work reports an effort to collect, classify and analyze SNVs that may affect the optimal response to currently approved drugs.

Results

An integrated approach was taken involving data mining across multiple information resources including databases containing drugs, drug targets, chemical structures, protein–ligand structure complexes, genetic and clinical variations as well as protein sequence alignment tools. We obtained 2640 SNVs of interest, most of which occur rarely in populations (minor allele frequency < 0.01). Clinical significance of only 9.56% of the SNVs is known in ClinVar, although 79.02% are predicted as deleterious. The examples here demonstrate that even if the mapped SNVs predicted as deleterious may not result in significant structural modifications, they can plausibly modify the protein–drug interactions, affecting selectivity and drug-binding affinity. Our analysis identifies potentially deleterious SNVs present on drug-binding residues that are relevant for further studies in the context of precision medicine.

Availability and Implementation

Data are available from Supplementary information file.

Supplementary information

Supplementary Tables S1–S5 are available at Bioinformatics online.
Riborex: fast and flexible identification of differential translation from Ribo-seq data
Authors: Li Wenzheng , Wang Weili , Uren Philip J , Penalva Luiz O F , Smith Andrew D
Published: January 2017

Motivation

Global analysis of translation regulation has recently been enabled by the development of Ribosome Profiling, or Ribo-seq, technology. This approach provides maps of ribosome activity for each expressed gene in a given biological sample. Measurements of translation efficiency are generated when Ribo-seq data is analyzed in combination with matched RNA-seq gene expression profiles. Existing computational methods for identifying genes with differential translation across samples are based on sound principles, but require users to choose between accuracy and speed.

Results

We present Riborex, a computational tool for mapping genome-wide differences in translation efficiency. Riborex shares a similar mathematical structure with existing methods, but has a simplified implementation. Riborex directly leverages established RNA-seq analysis frameworks for all parameter estimation, providing users with a choice among robust engines for these computations. The result is a method that is dramatically faster than available methods without sacrificing accuracy.

Availability and Implementation

https://github.com/smithlabcode/riborex

Supplementary information

Supplementary data are available at Bioinformatics online.
Accurate prediction of human essential genes using only nucleotide composition and association information
Authors: Guo Feng-Biao , Dong Chuan , Hua Hong-Li , Liu Shuo , Luo Hao , Zhang Hong-Wan , Jin Yan-Ting , Zhang Kai-Yue
Published: January 2017

Motivation

Previously constructed classifiers in predicting eukaryotic essential genes integrated a variety of features including experimental ones. If we can obtain satisfactory prediction using only nucleotide (sequence) information, it would be more promising. Three groups recently identified essential genes in human cancer cell lines using wet experiments and it provided wonderful opportunity to accomplish our idea. Here we improved the Z curve method into the λ-interval form to denote nucleotide composition and association information and used it to construct the SVM classifying model.

Results

Our model accurately predicted human gene essentiality with an AUC higher than 0.88 both for 5-fold cross-validation and jackknife tests. These results demonstrated that the essentiality of human genes could be reliably reflected by only sequence information. We re-predicted the negative dataset by our Pheg server and 118 genes were additionally predicted as essential. Among them, 20 were found to be homologues in mouse essential genes, indicating that some of the 118 genes were indeed essential, however previous experiments overlooked them. As the first available server, Pheg could predict essentiality for anonymous gene sequences of human. It is also hoped the λ-interval Z curve method could be effectively extended to classification issues of other DNA elements.

Availability and Implementation

http://cefg.uestc.edu.cn/Pheg

Supplementary information

Supplementary data are available at Bioinformatics online.