bluuebunny/crossref_metadata_2025 huggingface dataset:
Phosphorus and arsenic distributions in a seasonally stratified, iron- and manganese-rich lake: microbiological and geochemical controls
Authors: Hartland Adam , Andersen Martin S. , Hamilton David P.
Published: July 2015

Environmental context Despite being present at trace concentrations, arsenic and phosphorus are among the most important of freshwater contaminants. This research highlights the biogeochemical coupling of both elements in a New Zealand lake. We find that the mineralisation of organic residues coupled to the dissolution of colloidal iron and manganese hydroxides may be an important driver of the bioavailability of phosphorus and arsenic. Abstract Seasonal stratification in temperate lakes greater than a few metres deep provides conditions amenable to pronounced vertical zonation of redox chemistry. Such changes are particularly evident in eutrophic systems where high phytoplankton biomass often leads to seasonally established anaerobic hypolimnia and profound changes in geochemical conditions. In this study, we investigated the behaviour of trace elements in the water column of a seasonally stratified, eutrophic lake. Two consecutive years of data from Lake Ngapouri, North Island, New Zealand, demonstrate the occurrence of highly correlated profiles of phosphorus, arsenic, iron and manganese, all of which increased in concentration by 1–2 orders of magnitude within the anaerobic hypolimnion. Stoichiometric and mass-balance considerations demonstrate that increases in alkalinity in hypolimnetic waters were consistent with observed changes in sulfate, Fe and Mn concentrations with depth, corresponding to dissimilatory reduction of sulfate, FeIII and MnIV hydroxides. Thermodynamic constraints on Fe, Mn and Al solubility indicate that amorphous FeIII, MnIV hydroxides most probably controlled Fe and Mn in the surface mixed layer (~0 to 8m) whereas AlIII hydroxides were supersaturated throughout the entire system. Surface complexation modelling indicated that iron hydroxides (HFO) potentially dominated As speciation in the lake. It is likely that other colloidal phases such as allophanic clays also limited HPO42– activity, reducing competition for HAsO42– adsorption to iron hydroxides. This research highlights the coupling of P, As, Fe and Mn in Lake Ngapouri, and the apparent role of multiple colloidal phases in affecting P and As activity within overarching microbiological and geochemical processes.
Voltammetric tools for trace element speciation in fresh waters: methodologies, outcomes and future perspectives
Authors: Monticelli Damiano , Caprara Salvatore
Published: July 2015

Environmental context Trace elements are ubiquitous in natural waters where their levels are highly variable depending on natural factors and anthropogenic pollution. The chemical form of the element determines its behaviour in the environment and whether it is likely to pose a risk to environmental and human health. This paper focuses on elemental forms in freshwater systems: it reviews analytical methods, gathers available data, and assesses trends, needs and open issues in this field. Abstract Research in voltammetric speciation methods has been mainly driven by the research interests of the oceanographic scientific community and methods were subsequently adapted to freshwater conditions. Nonetheless, different processes, variability of geological, chemical, biological and ecological settings on the one side, and different human land and water uses on the other imply specific needs and a strong shift in concerns for inland waters in terms of investigated analytes. This review paper focuses on speciation of trace elements in freshwater by voltammetric techniques, giving information on and a critical assessment of the state of the art in this field. Methods determining covalently bound substituents, redox species and element forms differing in the nature of their complexed substituents were considered, according to the IUPAC definition of species. Three relevant topics are discussed: an overview of existing voltammetric speciation methods, with emphasis on practical features; current knowledge in the field of trace element speciation in freshwater bodies, organised by element and matrix; and future perspectives and needs for freshwater speciation studies. As a general outcome, a complete picture of trace element speciation in freshwater matrices is far from being achieved.
Dynamic epigenetic regulation of glioblastoma tumorigenicity through LSD1 modulation of MYC expression
Authors: Kozono David , Li Jie , Nitta Masayuki , Sampetrean Oltea , Gonda David , Kushwaha Deepa S. , Merzon Dmitry , Ramakrishnan Valya , Zhu Shan , Zhu Kaya , Matsui Hiroko , Harismendy Olivier , Hua Wei , Mao Ying , Kwon Chang-Hyuk , Saya Hideyuki , Nakano Ichiro , Pizzo Donald P. , VandenBerg Scott R. , Chen Clark C.
Published: July 2015

Significance

Glioblastoma is the most common type of adult brain cancer, with near-uniform fatality within 2 y of diagnosis. Therapeutic failure is thought to be related to small subpopulations of cells that exhibit tumorigenicity, the cellular capacity to reconstitute the entire tumor mass. One fundamental issue is whether tumorigenicity exists within a static subpopulation of cells or whether the capacity is stochastically acquired. We provide evidence that tumorigenicity is a cellular property that is durable yet undergoes low-frequency stochastic changes. We showed that these changes are driven by lysine-specific demethylase 1 (LSD1)-mediated epigenetic (heritable non-DNA sequence-altering) modifications that impact expression of key transcription factors, which in turn govern transitions between tumorigenic states. These findings harbor implications for glioblastoma therapeutic development.
Kazuo Ishiguro’s gentle transgression of tradition, myths and stereotypes
Authors: Nélis Noémie
Published: July 2015

The present article aims to provide a reading of Kazuo Ishiguro’s 1989 Booker Prize-winning novel The Remains of the Day that focuses on the author’s ‘gentle transgression’ of three local myths become international commodities: the myths of the English butler, the English country house and Englishness itself. It also examines how, in the process, the butler’s identity becomes an increasingly heterogeneous one, a “transindividuality” (Bessière 2010) potentially representative of a sedentary or “rooted” (Appiah 1997) form of critical cosmopolitanism. Ishiguro thus responds to the challenges of globalization, suggesting that a constantly questioned to-and-fro movement between the local and the global, each in turn enriching the other, might prevent the much-feared homogenization of cultures.
Amount classifiers in Chinese and the mass/count distinction
Authors: Liu Chen-Sheng Luther
Published: July 2015

In Chinese, temporary classifiers form together with classifiers likepiàn‘piece’,tuán‘something ball-shaped’,gǔ‘stream or stand’ andpài‘faction or clique’ a type of classifiers that has both mass and count forms. When occurring with the determinative quantifieryīto create a structure conveying the part-related reading, they appear in the ‘mass form’ (i.e., amount classifiers), but the ‘count form’ (i.e., number classifiers) when occurring with a genuine numeral. That is, the nominal mass/count distinction in Chinese is reflected at the classifier level as the distinction between the amount classifier and the number classifier. Moreover, this distinction is grammatical not ontological.
Indefinite article or numeral one?
Authors: Zhang Qingwen , Cheng Zhenquan , Tang Sze-Wing , Liu Hongyong
Published: July 2015

This paper investigatesiʔ5‘one’ in Shiposheng, a vernacular dialect spoken in the north of Guangdong Province. Thoughiʔ5in Shiposheng andyi‘one’ in Mandarin share similar usages, they behave differently when cooccurring with the demonstrative, i.e.,iʔ5in Shiposheng cannot follow the demonstrative as its Mandarin counterpart does. It is proposed that the numeral for ‘one’ in Shiposheng is grammaticalized to an indefinite article, whileyi‘one’ in Mandarin is still a numeral though it could be used as an indefinite article in some cases. The different behaviors of the Mandarinyi‘one’ and the Shiposhengiʔ5are due to their distinct grammatical status.
The partitive construction in Mandarin Chinese
Authors: Jin Jing
Published: July 2015

This paper investigates the semantic and syntactic properties of [N(oun)+de+Q(uantifier)] in Mandarin Chinese. Based on a comparison with the quantitive construction [Q+N], the paper advocates that [N+de+Q] is the Chinese partitive construction. Adopting a clausal approach to the syntactic derivation of partitives, it is hypothesized that Chinese partitives are formed via applying Predicate Inversion to a small clause that features a BELONG-type possession relationship. The difference between Chinese partitives and English-type partitives in terms of the surface word order is a result of a parametric variation with respect to whether the remnant of Predication Inversion undergoes further raising or not.
Syntactic position constrains cross-linguistic activation
Authors: Marull Crystal H.
Published: July 2015

There are two competing theories of bilingual lexical access — the language-selective access theory, which proposes that only the lexical items from the intended language are activated for selection during speech planning and comprehension (e.g., Costa, Santesteban, & Ivanova, 2006), and the language non-selective access theory, which proposes that both languages receive activation and compete for production (e.g., Kroll, Bobb, & Wodniecka, 2006). This study examines whether language-specific syntax — the syntactic positioning of a target word in a determiner phrase — can act as a language cue to modulate cross-linguistic activation and whether inhibition resolves competition (e.g., Green, 1998). In two cross-modal priming (+/−Rep) tasks, Spanish-English bilinguals were presented English sentences that were linearly congruent (Canonical Dative and of-Genitive) or incongruent (Dative Double Object and ’s-Genitive) with Spanish syntax and were prompted to make a lexical decision on a Spanish translation of the target word or a control word. The RTs revealed that participants were significantly slower in the incongruent condition (−Rep) than the congruent condition (−Rep) suggesting that language-specific syntax is a language cue that modulates cross-linguistic activation. When participants were prompted to repeat the sentences aloud (+Rep), the translation equivalent was expected to compete with the target word for production, yet no significant difference of RTs was found and the role of inhibition in speech production was not confirmed. Taken together, these findings support the language non-selective access model and further refine current theories of cross-linguistic activation and inhibitory control during bilingual language comprehension and production.
Deictic expressions in Darma (Almora)
Authors: Willis Oko Christina M.
Published: July 2015

This paper provides a description of the morphological composition and syntactic distribution of the spatial deictic system found in Darma a Tibeto-Burman language spoken in Uttarakhand, India. The description is informed by existing typologies of deictics and demonstratives (e.g. Levinson 1983; Diessel 1999, 2013; Senft 2004) with an eye towards identifying similar patterns in other Tibeto-Burman languages. In Darma, we find that the deictic roots can be meaningfully categorized into two groups based on the scale of reference: a distance-based scale (e.g. near and far), and a direction-based scale (e.g. up and down). These deictic roots combine with other morphemes to form sets of demonstratives that are categorized as Demonstrative Pronouns, Demonstrative Adverbs, and Demonstrative Quantifiers. In addition to the morphological structure of deictic elements, this paper explores the syntactic distribution of the deictic roots and combined demonstrative forms and suggests that a set of determiners is in the process of grammaticalizing. The discussion is geared towards contrasting the typology of demonstrative systems with the data attested in Darma and emphasizing topics that should be described in grammars of Tibeto-Burman languages.
Scoring a goal or an own-goal against disease?
Authors: El Refaie Elisabeth
Published: July 2015

Many contemporary public health campaigns use some form of metaphor. Studies into what makes this strategy effective typically focus on the ability of metaphors to attract attention and trigger conversations. Consequently, the question of how they might enhance or impede people’s understanding of the information conveyed is often overlooked. This article brings together key concepts in Conceptual Metaphor Theory with the latest findings in health communication to present a framework for describing metaphors in health promotion on the basis of their experiential, internal, external and narrative coherence. Using the comparative analysis of two children’s comics about tuberculosis as a small-scale case study, the paper argues that metaphor coherence is particularly important in health campaigns that aim to convey complex, new information. The paper ends with suggestions for validating the framework more broadly.
Prevalence and Hospital Discharge Status of Human Immunodeficiency Virus–Associated Pulmonary Arterial Hypertension in the United States
Authors: Henriques‐Forsythe Marshaleen , Annangi Srinadh , Farber Harrison W.
Published: July 2015

Pulmonary arterial hypertension (PAH) is a noninfectious complication of human immunodeficiency virus (HIV) infection that has gained in importance since the advent of antiretroviral therapy. HIV‐associated PAH (HIV‐PAH) has a higher prevalence than idiopathic PAH (IPAH), although the vascular pathology seen in HIV‐PAH is virtually identical to that seen in IPAH. Initiating therapy for PAH at an early stage is associated with a better prognosis; however, because of the nonspecific symptoms associated with PAH, the diagnosis is often delayed. In addition, because of the low prevalence of HIV‐PAH, routine screening for this condition has never been recommended. We hypothesize that the failure to create screening guidelines for HIV‐PAH has resulted in underdiagnosis of the condition. This, in turn, results in individuals with HIV‐PAH remaining undetected, allowing the disease to progress to more advanced stages or even remain unrecognized until death. If this hypothesis is correct, it may provide a strong argument for HIV‐PAH screening guidelines, because HIV‐PAH portends a poor prognosis and creates a significant economic burden if left untreated. To address this issue, we conducted a retrospective review of the National Hospital Discharge Survey data and the multiple‐cause mortality data to determine the prevalence of HIV‐PAH at hospital discharge and death. Using these large data sets, we observed that the prevalence of HIV‐PAH among HIV‐infected individuals at hospital discharge and death was significantly lower than the reported prevalence in the literature. In addition, we found that PAH was designated as the most common cause of mortality in patients with HIV‐PAH.
Cox rings of extremal rational elliptic surfaces
Authors: Artebani Michela , Garbagnati Alice , Laface Antonio
Published: July 2015

In this paper we determine a minimal set of generators for the Cox rings of extremal rational elliptic surfaces. Moreover, we develop a technique for computing the ideal of relations between them which allows us to provide a presentation of the Cox ring in most cases.
A finite basis theorem for difference-term varieties with a finite residual bound
Authors: Kearnes Keith , Szendrei Ágnes , Willard Ross
Published: July 2015

We prove that if

V

\mathcal V

is a variety of algebras (i.e., an equationally axiomatizable class of algebraic structures) in a finite language,

V

\mathcal V

has a difference term, and

V

\mathcal V

has a finite residual bound, then

V

\mathcal V

is finitely axiomatizable. This provides a common generalization of R. McKenzie’s finite basis theorem for congruence modular varieties with a finite residual bound, and R. Willard’s finite basis theorem for congruence meet-semidistributive varieties with a finite residual bound.
Comparison of 4 Admission Blood Pressure Indexes for Predicting
30-Day Mortality in Patients With ST-Segment Elevation Myocardial
Infarction
Authors: Ma Wen-fang , Liang Yan , Zhu Jun , Yang Yan-min , Tan Hui-qiong , Yu Li-tian , Gao Xin , Feng Guang-xun , Li Jian-dong
Published: July 2015

BACKGROUND

We compared admission systolic blood pressure (SBP), diastolic blood pressure (DBP), pulse pressure (PP), and mean arterial pressure (MAP) in predicting 30-day all-cause mortality in patients with ST-segment elevation myocardial infarction (STEMI) without cardiogenic shock.

METHODS

A retrospective study was performed in 7,033 consecutive STEMI patients. Multivariate-adjusted hazard ratios (HRs) with a 10mm Hg increment and quartiles of each blood pressure were determined by Cox proportional hazard analyses; Wald χ2 tests were used to compare the strength of relationships.

RESULTS

Totally 593 (8.4%) patients died during follow-up. Of 4 indexes, only SBP (HR 0.94 per 10mm Hg, 95% confidence interval (CI) 0.91 to 0.98; P = 0.001) and PP (HR 0.89 per 10 mmHg, 95% CI 0.85 to 0.94; P < 0.001) were significantly associated with 30-day all-cause mortality; these in the highest vs. lowest quartiles of SBP (≥140 vs. <110mm Hg) and PP (≥60 vs. <40mm Hg) had HRs of mortality of 0.70 (95% CI 0.55 to 0.87; P = 0.003) and 0.60 (95% CI 0.47 to 0.75; P < 0.001), respectively. Compared with SBP, PP was a better predictor for mortality no matter in men ( χ2 = 5.9 for per 10mm Hg, χ2 = 10.8 for quartiles) or women ( χ2 = 15.1 for per 10mm Hg, χ2 = 19.5 for quartiles), and the relationship remained significant after adjustment of SBP. There was a pattern of declining risk with increasing blood pressures for mortality, and this trend was mainly observed in age groups of more than 70 years.

CONCLUSIONS

Pulse pressure was an independent predictor of mortality in patients with STEMI, and low admission blood pressure should serve as a warning sign.
Predicting Risk of End-Stage Liver Disease in Antiretroviral-Treated Human Immunodeficiency Virus/Hepatitis C Virus-Coinfected Patients
Authors: Lo Re Vincent , Kallan Michael J. , Tate Janet P. , Lim Joseph K. , Goetz Matthew Bidwell , Klein Marina B. , Rimland David , Rodriguez-Barradas Maria C. , Butt Adeel A. , Gibert Cynthia L. , Brown Sheldon T. , Park Lesley S. , Dubrow Robert , Reddy K. Rajender , Kostman Jay R. , Justice Amy C. , Localio A. Russell
Published: July 2015

Background.  End-stage liver disease (ESLD) is an important cause of morbidity among human immunodeficiency virus (HIV)/hepatitis C virus (HCV)-coinfected patients. Qua.jpegying the risk of this outcome over time could help determine which coinfected patients should be targeted for risk factor modification and HCV treatment. We evaluated demographic, clinical, and laboratory variables to predict risk of ESLD in HIV/HCV-coinfected patients receiving antiretroviral therapy (ART).

Methods.  We conducted a retrospective cohort study among 6016 HIV/HCV-coinfected patients who received ART within the Veterans Health Administration between 1997 and 2010. The main outcome was incident ESLD, defined by hepatic decompensation, hepatocellular carcinoma, or liver-related death. Cox regression was used to develop prognostic models based on baseline demographic, clinical, and laboratory variables, including FIB-4 and aspartate aminotransferase-to-platelet ratio index, previously validated markers of hepatic fibrosis. Model performance was assessed by discrimination and decision curve analysis.

Results.  Among 6016 HIV/HCV patients, 532 (8.8%) developed ESLD over a median of 6.6 years. A model comprising FIB-4 and race had modest discrimination for ESLD (c-statistic, 0.73) and higher net benefit than alternative strategies of treating no or all coinfected patients at relevant risk thresholds. For FIB-4 >3.25, ESLD risk ranged from 7.9% at 1 year to 26.0% at 5 years among non-blacks and from 2.4% at 1 year to 14.0% at 5 years among blacks.

Conclusions.  Race and FIB-4 provided important predictive information on ESLD risk among HIV/HCV patients. Estimating risk of ESLD using these variables could help direct HCV treatment decisions among HIV/HCV-coinfected patients.
Protein binding and methylation on looping chromatin accurately predict distal regulatory interactions
Authors: Whalen Sean , Truty Rebecca M. , Pollard Katherine S.
Published: July 2015

Identifying the gene targets of distal regulatory sequences is a challenging problem with the potential to illuminate the causal underpinnings of complex diseases. However, current experimental methods to map enhancer-promoter interactions genome-wide are limited by their cost and complexity. We presentTargetFinder, a computational method that reconstructs a cell’s three-dimensional regulatory landscape from two-dimensional genomic features.TargetFinderachieves outstanding predictive accuracy across diverse cell lines with a false discovery rate up to fifteen times smaller than common heuristics, and reveals that distal regulatory interactions are characterized by distinct signatures of protein interactions and epigenetic marks on the DNA loop between an active enhancer and targeted promoter. Much of this signature is shared across cell types, shedding light on the role of chromatin organization in gene regulation and establishingTargetFinderas a method to accurately map long-range regulatory interactions using a small number of easily acquired datasets.
Examining the cultural value of festivals
Authors: George Jodie
Published: July 2015

Purpose

– Within Australia, cultural festivals focusing on music, food and art represent important social and economic opportunities for rural communities. However, tensions may also arise within communities where stakeholder ideologies are at odds regarding the place identity being presented for consumption by tourism practices. Thus, using Mitchell’s model of creative destruction/creative enhancement as a theoretical framework and through qualitative analysis, the purpose of this paper is to critically examine three South Australian festivals from multiple perspectives, to identify what relevant stakeholders consider festivals contribute to the community and how this may impact on the success of the festival itself.

Design/methodology/approach

– Using Mitchell’s model of creative destruction/creative enhancement as a theoretical framework and through qualitative analysis, this research critically examines three South Australian festivals from multiple perspectives, to identify what relevant stakeholders consider festivals contribute to the community and how this may impact on the success of the festival itself.

Findings

– Findings suggest that those communities who present a more complex understanding of the “rural idyll” through the integration of multiple local products will experience greater success, both for internal and external audiences.

Originality/value

– This research represents a unique contribution to the literature on festivals by combining the theoretical construct of cultural value with Mitchell’s model of creative destruction and creative enhancement, particularly within South Australia where little such work has been one, despite the fact that it presents itself as the “Festival State”.
Hecke characters associated to Drinfeld modular forms
Authors: Böckle Gebhard , Centeleghe Tommaso
Published: July 2015

In this article we explain how the results in our previous article on ‘algebraic Hecke characters and compatible systems of mod$p$Galois representations over global fields’ allow one to attach a Hecke character to every cuspidal Drinfeld modular eigenform from its associated crystal that was constructed in earlier work of the author. On the technical side, we prove along the way a number of results on endomorphism rings of${\it\tau}$-sheaves and crystals. These are needed to exhibit the close relation between Hecke operators as endomorphisms of crystals on the one side and Frobenius automorphisms acting on étale sheaves associated to crystals on the other. We also present some partial results on the ramification of Hecke characters associated to Drinfeld modular eigenforms. An important phenomenon absent from the case of classical modular forms is that ramification can also result from places of modular curves of good but non-ordinary reduction. In an appendix, jointly with Centeleghe we prove some basic results on$p$-adic Galois representations attached to$\text{GL}_{2}$-type cuspidal automorphic forms over global fields of characteristic $p$.
A mirror theorem for toric stacks
Authors: Coates Tom , Corti Alessio , Iritani Hiroshi , Tseng Hsian-Hua
Published: July 2015

We prove a Givental-style mirror theorem for toric Deligne–Mumford stacks${\mathcal{X}}$. This determines the genus-zero Gromov–Witten invariants of${\mathcal{X}}$in terms of an explicit hypergeometric function, called the$I$-function, that takes values in the Chen–Ruan orbifold cohomology of${\mathcal{X}}$.
Experimental analysis of the relationship between reverberant acoustic intensity and energy density inside long rooms
Authors: Visentin Chiara , Prodi Nicola , Valeau Vincent , Picaut Judicaël
Published: July 2015

In this paper, the validity of the Fick's law of diffusion in room acoustics is experimentally investigated inside long rooms. The room-acoustics diffusion model relies on Fick's law stating a proportionality relationship between sound intensity and energy density gradient inside a room through a constant diffusion coefficient. This relationship is investigated in the stationary state for the particular case of long rooms with different amounts of boundary scattering. Measurements were performed inside a 1:16 scale model, using a p-u sound intensity probe (calibrated with digital filters) to collect concurrent data in terms of sound pressure and axial velocity components. Then for each receiver position, sound intensity and energy density gradient were derived. The results show that inside long rooms the diffusion coefficient is not a constant but increases with the distance from the source with a slope depending on the scattering coefficient of the walls. Numerical simulations of the enclosures were performed too by using a sound particle-tracing code; a substantial agreement with the experimental findings is observed. The results imply that for such long enclosures, the diffusion model should consider a space-varying diffusion coefficient to be more consistent with real phenomena.
Recent hiatus caused by decadal shift in Indo-Pacific heating
Authors: Nieves Veronica , Willis Josh K. , Patzert William C.
Published: July 2015

Looking for the missing heat

Global warming apparently slowed, or even stopped, during the first decade of the 21st century. This pause is commonly called the “hiatus.” We know, however, that Earth's climate system is accumulating excess solar energy owing to the build-up of greenhouse gases in the atmosphere. Where, then, has this energy gone if not into the air? Nieves
et al.
find that over this period, the surface Pacific Ocean has cooled but the upper Indian and Southern Oceans have warmed. Thus, the decade-long hiatus that began in 2003 would appear to be the result of a redistribution of heat within the ocean, rather than a change in the whole-Earth warming rate.

Science
, this issue p.
532
Rock physics of fibrous rocks akin to Roman concrete explains uplifts at Campi Flegrei Caldera
Authors: Vanorio Tiziana , Kanitpanyacharoen Waruntorn
Published: July 2015

Cementing Roman concrete to a caldera

Ancient concrete would seem to have little to do with volcano geology. However, Vanorio and Kanitpanyacharoen found similarities between the caprock of the Campi Flegrei caldera near Naples, Italy, and the Roman-era concrete for which the region was known. Both materials require a similar set of chemical reactions to give it the high strength caused by microstructures of intertwining fibrous minerals. The high strength of the natural rock explains the ability of the caldera to withstand periods of high-rate uplift without eruption. The Romans living in the caldera, where the town of Pozzuoli is today, may have been trying to mimic nature to produce this iconic material.

Science
, this issue p.
617
Draft Genome Sequence of a Natural Root Isolate, Bacillus subtilis UD1022, a Potential Plant Growth-Promoting Biocontrol Agent
Authors: Bishnoi Usha , Polson Shawn W. , Sherrier D. Janine , Bais Harsh P.
Published: July 2015

Bacillus subtilis
, which belongs to the phylum
Firmicutes
, is the most widely studied Gram-positive model organism. It is found in a wide variety of environments and is particularly abundant in soils and in the gastrointestinal tracts of ruminants and humans. Here, we present the complete genome sequence of the newly described
B. subtilis
strain UD1022. The UD1022 genome consists of a 4.025-Mbp chromosome, and other major findings from our analysis will provide insights into the genomic basis of it being a plant growth-promoting rhizobacterium (PGPR) with biocontrol potential.
Complete Genome Sequence of a CTX-M-15-Producing Klebsiella pneumoniae Outbreak Strain from Multilocus Sequence Type 514
Authors: Becker Laura , Bunk Boyke , Eller Christoph , Steglich Matthias , Pfeifer Yvonne , Werner Guido , Nübel Ulrich
Published: July 2015

We report here the genome sequence of a multidrug-resistant
Klebsiella pneumoniae
strain, which caused an outbreak in a neonatal ward in 2011. The genome consists of a single chromosome (5,278 kb) and three plasmids (362 kb, 5 kb, and 4 kb).
Genome Sequence of
Vibrio
VPAP30, Isolated from an Episode of Massive Mortality of Reared Larvae of the Scallop
Argopecten purpuratus
Authors: Rojas Rodrigo , Miranda Claudio D. , Romero Jaime , Asenjo Freddy , Valderrama Katherinne , Segovia Cristopher , Ugalde Juan A. , Santander Javier
Published: July 2015

We report here the 5.167-Mbp draft genome sequence of
Vibrio
VPAP30, isolated from an
Argopecten purpuratus
larval culture.
Vibrio
VPAP30 is the etiological agent of a vibriosis outbreak causing a complete collapse of a larval culture of the scallop
A. purpuratus
, which occurred in a commercial hatchery in Chile.
Genome Sequence of
Arthrobacter
sp. YC-RL1, an Aromatic Compound-Degrading Bacterium
Authors: Ren Lei , Shi Yanhua , Jia Yang , Yan Yanchun
Published: July 2015

We report the 4.04-Mb draft genome sequence of
Arthrobacter
sp. YC-RL1, an aromatic compound-degrading bacterium. YC-RL1 could degrade a wide range of aromatic compounds, including naphthaline, 1,2,3,4-tetrachlorobenzene, fluorene, 4-nitrophenol, bisphenol A, biphenyl, and
p
-xylene. The genome sequence of YC-RL1 will promote the investigation of the biodegradation of aromatic compounds.
Sedentary time is not independently related to postural stability or leg strength in women 50–67 years old
Authors: Willoughby Taura , Copeland Jennifer L.
Published: July 2015

Most research on sedentary behaviour has focused on cardiometabolic outcomes and markers of metabolic dysfunction, while neuromuscular outcomes have received less attention. The objective of the present study was to determine whether sedentary time is negatively associated with laboratory-based measures of lower body muscular strength and postural stability in middle-aged women. Forty-nine women (56.6 ± 4.1 years) participated in the study. Participants wore an ActiGraph GT3X accelerometer for 7 days to quantify sedentary time and physical activity. Following a familiarization session, assessments of lower body muscular strength and postural stability were performed. Peak torque of knee extensors and flexors was assessed using an isokinetic dynamometer. Postural stability was assessed using computerized dynamic posturography and a composite equilibrium score (CES) was calculated. Participants spent 9.4 ± 1.3 h per day (65% of wear time) sedentary and 28.2 ± 17.3 min per day (3.3% of wear time) in moderate to vigorous physical activity (MVPA). Postural stability and relative peak torque of the knee flexors were significantly associated with time spent sedentary (r = –0.35, p = 0.01 and r = –0.31, p = 0.03, respectively). Multiple linear regression analyses showed that after adjusting for MVPA, sedentary time was not significantly related to either CES or peak torque of the knee extensors or flexors. In contrast to our hypothesis, postural stability and leg strength were not independently related to sedentary time. While sedentary behaviour may be an important risk factor for cardiometabolic disease, the present results suggest MVPA may be more important to neuromuscular outcomes.
Swelling phenomena and effective stress in compacted expansive clays
Authors: Mašín David , Khalili Nasser
Published: July 2015

The central aim of this paper is to discuss the applicability of the effective stress principle as defined by Terzaghi (total stress minus pore-water pressure) to predict the behaviour of expansive clay aggregates. Phenomena occurring between individual clay minerals are reviewed first at the molecular level obtained in the colloid science research. In particular, it is noted that, for interparticle distances higher than approximately 1.5 nm, the pore-water pressure in the bulk equilibrium solution forms an additive component of the interparticle disjoining pressure. It is concluded that for these distances Terzaghi’s effective stress principle should be adequate to describe the clay behaviour. To support these developments, an extensive experimental database of nine different sodium and calcium bentonites available in the published literature was analysed. With the aid of double structure constitutive modelling, procedures were developed to extract information about the behaviour of clay aggregates from the experimental measurements. It was then shown that unconfined water retention curves, swelling pressure tests, swelling under constant load tests, and mechanical unloading tests are all uniquely related in terms of the dependency of dry density (or void ratio) of clay aggregate versus mean effective stress. By considering reversibility of aggregate behaviour and full saturation of aggregates, this implies that the effective stress principle is a valid way of predicting expansive clay aggregate volumetric deformation.
Exploring phlebotomy technique as a pre-analytical factor in proteomic analyses by mass spectrometry
Authors: Penn Andrew M. , Lu Linghong , Chambers Andrew G. , Balshaw Robert F. , Morrison Jaclyn L. , Votova Kristine , Wood Eileen , Smith Derek S. , Lesperance Maria , del Zoppo Gregory J. , Borchers Christoph H.
Published: July 2015

Multiple reaction monitoring mass spectrometry (MRM-MS) is an emerging technology for blood biomarker verification and validation; however, the results may be influenced by pre-analytical factors. This exploratory study was designed to determine if differences in phlebotomy techniques would significantly affect the abundance of plasma proteins in an upcoming biomarker development study. Blood was drawn from 10 healthy participants using four techniques: (1) a 20-gauge IV with vacutainer, (2) a 21-gauge direct vacutainer, (3) an 18-gauge butterfly with vacutainer, and (4) an 18-gauge butterfly with syringe draw. The abundances of a panel of 122 proteins (117 proteins, plus 5 matrix metalloproteinase (MMP) proteins) were targeted by LC/MRM-MS. In addition, complete blood count (CBC) data were also compared across the four techniques. Phlebotomy technique significantly affected 2 of the 11 CBC parameters (red blood cell count, p = 0.010; hemoglobin concentration, p = 0.035) and only 12 of the targeted 117 proteins (p < 0.05). Of the five MMP proteins, only MMP7 was detectable and its concentration was not significantly affected by different techniques. Overall, most proteins in this exploratory study were not significantly influenced by phlebotomy technique; however, a larger study with additional patients will be required for confirmation.
Interest Point Detection in 3D Point Cloud Data Using 3D Sobel-Harris Operator
Authors: Hafiz Dina A. , Youssef Bayumy A. B. , Sheta Walaa M. , Hassan Hanan Ali
Published: July 2015

Manual selection of features from massive unstructured point cloud data is a very time-consuming task that requires a considerable amount of human intervention. This work is motivated by the need of fast and simple algorithm to obtain robust, stable and well-localized interest points that are used for subsequent processing in computer vision real-time applications. This paper presents an algorithm for detection of interest points in three-dimensional (3D) point cloud data by using a combined 3D Sobel–Harris operator. The proposed algorithm is compared with six state-of-the-art approaches used to identify the true feature points. Extensive experiments were carried out using synthetic benchmark and real datasets. The datasets were selected with different sizes, features and scales. The results were evaluated against human generated ground truth and predefined feature points. Three measures were used to evaluate the algorithm accuracy, namely localization accuracy Le, False Positive Error (FPE) and False Negative Errors (FNE). Also, the complexity analysis of the proposed algorithm is presented. The results show that the proposed algorithm can identify the interest points with accepted accuracy. It works directly on point cloud datasets and shows superiority when compared with other methods work on 3D mesh data.
Toward a mathematical theory of behavioral-social dynamics for pedestrian crowds
Authors: Bellomo Nicola , Gibelli Livio
Published: July 2015

This paper presents a new approach to behavioral-social dynamics for pedestrian crowds by suitable development of mathematical tools of the kinetic theory. It is shown how pedestrians heterogeneity and the propagation of local unusual behaviors in the crowd can be accounted for. The proposed model is applied to the study of two groups of pedestrians walking in opposite directions in a crowded street and its predictive ability is demonstrated by showing that emerging behaviors, such as pedestrian segregation, can be depicted.
Multiscale modelling of intestinal crypt organization and carcinogenesis
Authors: Fletcher Alexander G. , Murray Philip J. , Maini Philip K.
Published: July 2015

Colorectal cancers are the third most common type of cancer. They originate from intestinal crypts, glands that descend from the intestinal lumen into the underlying connective tissue. Normal crypts are thought to exist in a dynamic equilibrium where the rate of cell production at the base of a crypt is matched by that of loss at the top. Understanding how genetic alterations accumulate and proceed to disrupt this dynamic equilibrium is fundamental to understanding the origins of colorectal cancer. Colorectal cancer emerges from the interaction of biological processes that span several spatial scales, from mutations that cause inappropriate intracellular responses to changes at the cell/tissue level, such as uncontrolled proliferation and altered motility and adhesion. Multiscale mathematical modelling can provide insight into the spatiotemporal organisation of such a complex, highly regulated and dynamic system. Moreover, the aforementioned challenges are inherent to the multiscale modelling of biological tissue more generally. In this review we describe the mathematical approaches that have been applied to investigate multiscale aspects of crypt behavior, highlighting a number of model predictions that have since been validated experimentally. We also discuss some of the key mathematical and computational challenges associated with the multiscale modelling approach. We conclude by discussing recent efforts to derive coarse-grained descriptions of such models, which may offer one way of reducing the computational cost of simulation by leveraging well-established tools of mathematical analysis to address key problems in multiscale modelling.
A finite field hypergeometric function associated to eigenvalues of a Siegel eigenform
Authors: McCarthy Dermot , Papanikolas Matthew A.
Published: July 2015

Although links between values of finite field hypergeometric functions and eigenvalues of elliptic modular forms are well known, we establish in this paper that there are also connections to eigenvalues of Siegel modular forms of higher degree. Specifically, we relate the eigenvalue of the Hecke operator of index p of a Siegel eigenform of degree 2 and level 8 to a special value of a 4F3-hypergeometric function.
Abstraction in Fixpoint Logic
Authors: Cranen Sjoerd , Gazda Maciej , Wesselink Wieger , Willemse Tim A. C.
Published: July 2015

We present a theory of abstraction for the framework of parameterised Boolean equation systems, a first-order fixpoint logic. Parameterised Boolean equation systems can be used to solve a variety of problems in verification. We study the capabilities of the abstraction theory by comparing it to an abstraction theory for Generalised Kripke modal Transition Systems (GTSs). We show that for model checking the modal μ-calculus, our abstractions can be exponentially more succinct than GTSs and our theory is as complete as the GTS framework for abstraction. Furthermore, we investigate the completeness of our theory irrespective of the encoded decision problem. We illustrate the potential of our theory through case studies using the first-order modal μ-calculus and a real-time extension thereof, conducted using a prototype implementation of a new syntactic transformation for parameterised Boolean equation systems.
SonicAIR
Authors: Baharin Hanif , Viller Stephen , Rintel Sean
Published: July 2015

Sonic Atomic Interaction Radio (SonicAIR) is an ambient awareness technology probe designed to explore how connecting the soundscapes of friends or family members might reduce the isolation of seniors living independently. At its core, SonicAIR instruments kitchen activity sites to produce an always-on real-time aural representation of remote domestic rhythms. This article reports how users in two pilot SonicAIR deployments used the sounds as resources for recognizing comfortable narratives of sociability. Used alongside telecare monitoring, such technologized interaction might enable older people to engage in community-oriented soundscape narratives of shared social responsibility.
Aging-Aware Compilation for GP-GPUs
Authors: Lotfi Atieh , Rahimi Abbas , Benini Luca , Gupta Rajesh K.
Published: July 2015

General-purpose graphic processing units (GP-GPUs) offer high computational throughput using thousands of integrated processing elements (PEs). These PEs are stressed during workload execution, and negative bias temperature instability (NBTI) adversely affects their reliability by introducing new delay-induced faults. However, the effect of these delay variations is not uniformly spread across the PEs: some are affected more—hence less reliable—than others. This variation causes significant reduction in the lifetime of GP-GPU parts. In this article, we address the problem of “wear leveling” across processing units to mitigate lifetime uncertainty in GP-GPUs. We propose innovations in the static compiled code that can improve healing in PEs and stream cores (SCs) based on their degradation status. PE healing is a fine-grained very long instruction word (VLIW) slot assignment scheme that balances the stress of instructions across the PEs within an SC. SC healing is a coarse-grained workload allocation scheme that distributes workload across SCs in GP-GPUs. Both schemes share a common property: they adaptively shift workload from less reliable units to more reliable units, either spatially or temporally. These software schemes are based on online calibration with NBTI monitoring that equalizes the expected lifetime of PEs and SCs by regenerating adaptive compiled codes to respond to the specific health state of the GP-GPUs. We evaluate the effectiveness of the proposed schemes for various OpenCL kernels from the AMD APP SDK on Evergreen and Southern Island GPU architectures. The aging-aware healthy kernels generated by the PE (or SC) healing scheme reduce NBTI-induced voltage threshold shift by 30% (77% in the case of SCs), with no (moderate) performance penalty compared to the naive kernels.
Some Hard Families of Parameterized Counting Problems
Authors: Jerrum Mark , Meeks Kitty
Published: July 2015

We consider parameterized subgraph counting problems of the following form: given a graph
G
, how many
k
-tuples of its vertices induce a subgraph with a given property? A number of such problems are known to be #W[1]-complete; here, we substantially generalize some of these existing results by proving hardness for two large families of such problems. We demonstrate that it is #W[1]-hard to count the number of
k
-vertex subgraphs having any property where the number of distinct edge densities of labeled subgraphs that satisfy the property is
o
(
k
2
). In the special case in which the property in question depends only on the number of edges in the subgraph, we give a strengthening of this result, which leads to our second family of hard problems.
Mutual Dimension
Authors: Case Adam , Lutz Jack H.
Published: July 2015

We define the lower and upper
mutual dimensions
mdim
(
x
:
y
) and
Mdim
(
x
:
y
) between any two points
x
and
y
in Euclidean space. Intuitively, these are the lower and upper densities of the algorithmic information shared by
x
and
y
. We show that these quantities satisfy the main desiderata for a satisfactory measure of mutual algorithmic information. Our main theorem, the
data processing inequality
for mutual dimension, says that if
f
: R

m

→ R

n

is computable and Lipschitz, then the inequalities
mdim
(
f
(
x
):
y
) ≤
mdim
(
x
:
y
) and
Mdim
(
f
(
x
):
y
) ≤
Mdim
(
x
:
y
) hold for all
x
∈ R

m

and
y
∈ R

t

. We use this inequality and related inequalities that we prove in like fashion to establish conditions under which various classes of computable functions on Euclidean space preserve or otherwise transform mutual dimensions between points.
Real-Time Monitoring of Critical Care Analytes in the Bloodstream with Chemical Sensors: Progress and Challenges
Authors: Frost Megan C. , Meyerhoff Mark E.
Published: July 2015

We review approaches and challenges in developing chemical sensor-based methods to accurately and continuously monitor levels of key analytes in blood related directly to the status of critically ill hospitalized patients. Electrochemical and optical sensor-based technologies have been pursued to measure important critical care species in blood [i.e., oxygen, carbon dioxide, pH, electrolytes (K+, Na+, Cl−, etc.), glucose, and lactate] in real-time or near real-time. The two main configurations examined to date for achieving this goal have been intravascular catheter sensors and patient attached ex vivo sensors with intermittent blood sampling via an attached indwelling catheter. We discuss the status of these configurations and the main issues affecting the accuracy of the measurements, including cell adhesion and thrombus formation on the surface of the sensors, sensor drift, sensor selectivity, etc. Recent approaches to mitigate these nagging performance issues that have prevented these technologies from clinical use are also discussed.