bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abnormal SDS‐PAGE migration of cytosolic proteins can identify domains and mechanisms that control surfactant binding
Authors: Shi Yunhua , Mowery Richard A. , Ashley Jonathan , Hentz Michelle , Ramirez Alejandro J. , Bilgicer Basar , Slunt‐Brown Hilda , Borchelt David R. , Shaw Bryan F. 
Published: June 2012

AbstractThe amino acid substitution or post‐translational modification of a cytosolic protein can cause unpredictable changes to its electrophoretic mobility during SDS‐PAGE. This type of “gel shifting” has perplexed biochemists and biologists for decades. We identify a mechanism for “gel shifting” that predominates among a set of ALS (amyotrophic lateral sclerosis) mutant hSOD1 (superoxide dismutase) proteins, post‐translationally modified hSOD1 proteins, and homologous SOD1 proteins from different organisms. By first comparing how 39 amino acid substitutions throughout hSOD1 affected SDS‐PAGE migration, we found that substitutions that caused gel shifting occurred within a single polyacidic domain (residues ∼80–101), and were nonisoelectric. Substitutions that decreased the net negative charge of domain 80–101 increased migration; only one substitution increased net negative charge and slowed migration. Capillary electrophoresis, circular dichroism, and size exclusion chromatography demonstrated that amino acid substitutions increase migration during SDS‐PAGE by promoting the binding of three to four additional SDS molecules, without significantly altering the secondary structure or Stokes radius of hSOD1‐SDS complexes. The high negative charge of domain 80–101 is required for SOD1 gel shifting: neutralizing the polyacidic domain (via chimeric mouse‐human SOD1 fusion proteins) inhibited amino acid substitutions from causing gel shifting. These results demonstrate that the pattern of gel shifting for mutant cytosolic proteins can be used to: (i) identify domains in the primary structure that control interactions between denatured cytosolic proteins and SDS and (ii) identify a predominant chemical mechanism for the interaction (e.g., hydrophobic vs. electrostatic).
Abstractions of non-interference security: probabilistic versus possibilistic
Authors: Hoang T. S. , McIver A. K. , Meinicke L. , Morgan C. C. , Sloane A. , Susatyo E. 
Published: June 2012

Abstract

The Shadow Semantics (Morgan, Math Prog Construction, vol 4014, pp 359–378,
2006
; Morgan, Sci Comput Program 74(8):629–653,
2009
) is a possibilistic (qualitative) model for noninterference security. Subsequent work (McIver et al., Proceedings of the 37th international colloquium conference on Automata, languages and programming: Part II,
2010
) presents a similar but more general
quantitative
model that treats probabilistic information flow. Whilst the latter provides a framework to reason about quantitative security risks, that extra detail entails a significant overhead in the verification effort needed to achieve it. Our first contribution in this paper is to study the relationship between those two models (qualitative and quantitative) in order to understand when qualitative Shadow proofs can be “promoted” to quantitative versions, i.e. in a probabilistic context. In particular we identify a subset of the Shadow’s refinement theorems that, when interpreted in the quantitative model, still remain valid even in a context where a passive adversary may perform probabilistic analysis. To illustrate our technique we show how a semantic analysis together with a syntactic restriction on the protocol description, can be used so that purely qualitative reasoning can nevertheless verify probabilistic refinements for an important class of security protocols. We demonstrate the semantic analysis by implementing the Shadow semantics in Rodin, using its special-purpose refinement provers to generate (and discharge) the required proof obligations (Abrial et al., STTT 12(6):447–466,
2010
). We apply the technique to some small examples based on secure multi-party computations.
On energetics and inertial-range scaling laws of two-dimensional magnetohydrodynamic turbulence
Authors: Blackbourn Luke A. K. , Tran Chuong V. 
Published: June 2012

AbstractWe study two-dimensional magnetohydrodynamic turbulence, with an emphasis on its energetics and inertial-range scaling laws. A detailed spectral analysis shows that dynamo triads (those converting kinetic into magnetic energy) are associated with a direct magnetic energy flux while anti-dynamo triads (those converting magnetic into kinetic energy) are associated with an inverse magnetic energy flux. As both dynamo and anti-dynamo interacting triads are integral parts of the direct energy transfer, the anti-dynamo inverse flux partially neutralizes the dynamo direct flux, arguably resulting in relatively weak direct energy transfer and giving rise to dynamo saturation. This result is consistent with a qualitative prediction of energy transfer reduction due to Alfvén wave effects by the Iroshnikov–Kraichnan theory (which was originally formulated for magnetohydrodynamic turbulence in three dimensions). We numerically confirm the correlation between dynamo action and direct magnetic energy flux and investigate the applicability of quantitative aspects of the Iroshnikov–Kraichnan theory to the present case, particularly its predictions of energy equipartition and ${k}^{\ensuremath{-} 3/ 2} $ spectra in the energy inertial range. It is found that for turbulence satisfying the Kraichnan condition of magnetic energy at large scales exceeding total energy in the inertial range, the kinetic energy spectrum, which is significantly shallower than ${k}^{\ensuremath{-} 3/ 2} $, is shallower than its magnetic counterpart. This result suggests no energy equipartition. The total energy spectrum appears to depend on the energy composition of the turbulence but is clearly shallower than ${k}^{\ensuremath{-} 3/ 2} $ for $r\approx 2$, even at moderate resolutions. Here $r\approx 2$ is the magnetic-to-kinetic energy ratio during the stage when the turbulence can be considered fully developed. The implication of the present findings is discussed in conjunction with further numerical results on the dependence of the energy dissipation rate on resolution.
Wicking of a liquid bridge connected to a moving porous surface
Authors: Gat A. D. , Navaz H. K. , Gharib M. 
Published: June 2012

AbstractWe study the coupled problem of a liquid bridge connected to a porous surface and an impermeable surface, where the gap between the surfaces is an externally controlled function of time. The relative motion between the surfaces influences the pressure distribution and geometry of the liquid bridge, thus affecting the shape of liquid penetration into the porous material. Utilizing the lubrication approximation and Darcy’s phenomenological law, we obtain an implicit integral relation between the relative motion between the surfaces and the shape of liquid penetration. A method to control the shape of liquid penetration is suggested and illustrated for the case of conical penetration shapes with an arbitrary cone opening angle. We obtain explicit analytic expressions for the case of constant relative speed of the surfaces as well as for the relative motion between the surfaces required to create conical penetration shapes. Our theoretical results are compared with experiments and reasonable agreement between the analytical and experimental data is observed.
A RESTRICTION OF EUCLID
Authors: CAIRNS GRANT , HO NHAN BAO 
Published: June 2012

AbstractEuclid is a well-known two-player impartial combinatorial game. A position in Euclid is a pair of positive integers and the players move alternately by subtracting a positive integer multiple of one of the integers from the other integer without making the result negative. The player who makes the last move wins. There is a variation of Euclid due to Grossman in which the game stops when the two entries are equal. We examine a further variation which we called M-Euclid where the game stops when one of the entries is a positive integer multiple of the other. We solve the Sprague–Grundy function for M-Euclid and compare the Sprague–Grundy functions of the three games.
SOME PROPERTIES OF A SEQUENCE ANALOGOUS TO EULER NUMBERS
Authors: SUN ZHI-HONG 
Published: June 2012

AbstractLet $\{U_n\}$ be given by $U_0=1$ and $U_n=-2\sum _{k=1}^{[n/2]} \binom n{2k}U_{n-2k}\ (n\ge 1)$, where $[\cdot ]$ is the greatest integer function. Then $\{U_n\}$ is analogous to the Euler numbers and $U_{2n}=3^{2n}E_{2n}(\frac 13)$, where $E_m(x)$ is the Euler polynomial. In a previous paper we gave many properties of $\{U_n\}$. In this paper we present a summation formula and several congruences involving $\{U_n\}$.
‘Singing Stones’: Contexting Body-Language in Romano-British Iconography
Authors: Aldhouse-Green Miranda 
Published: June 2012

AbstractTwo stone sculptures from Caerwent — a disembodied human head and a seated female figure — are the focus of this article. Using icon-theory, it is proposed that the Caerwent sculptures (albeit recovered from different chronological horizons) were perhaps produced at the same time, maybe even by a single stonemason. Issues of materiality, including choice of stone and style, are seen as key to their understanding, in terms of Silurian identity and religion. Moreover, the emphasis on mouths and ears invites interpretation of these images as those of speaking and listening Oracles, conduits between earthly and spiritual worlds.
Habitat occupancy of the Dusky-legged Guan in the lower delta of the Paraná River, Argentina
Authors: MALZOF SILVINA L. , BOLKOVIC MARIA L. , THOMPSON JEFFREY J. , QUINTANA RUBEN D. 
Published: June 2012

SummaryThe Dusky-legged Guan Penelope obscura is the southernmost species of the family Cracidae, reaching its southern distributional limit in the delta of the Paraná River. Habitat loss, together with uncontrolled harvest, has led to local-scale decreases or extirpation of the species, but no quantitative evaluation of habitat preferences has been made. We surveyed Dusky-legged Guans in the Delta del Paraná Biosphere Reserve, Argentina, by motorboat along 543.9 km of nine waterways during both January and July 2009 and used occupancy modelling to estimate habitat and seasonal effects on occupancy. Detectability was 21–22% on average and occupancy estimates were highly variable within habitats, but highest in secondary forest, followed by mature plantation, and lowest in occupied residences. There were no significant differences in occupancy or detectability among habitats or seasonally. There was a strong positive effect of length of riparian habitat segments on occupancy and detectability. Habitat management efforts should address increasing the suitability of mature plantation forest for guans by increasing their similarity to native forest in structure and composition. Furthermore, we illustrate that surveys by boat can be logistically effective for surveying cracids associated with riverine habitats and that it is important to account for incomplete detectability since in our case failing to do so would have underestimated occupancy by 78–79% on average. Given this, the use of commonly accepted methodologies for surveying cracids that do not account for incomplete detectability should be reconsidered and methodologies that can produce robust, reliable estimates applied.
The roles of cloud drop effective radius and LWP in determining rain properties in marine stratocumulus
Authors: Rosenfeld Daniel , Wang Hailong , Rasch Philip J. 
Published: June 2012

Numerical simulations described in previous studies showed that adding cloud condensation nuclei to marine stratocumulus can prevent their breakup from closed into open cells. Additional analyses of the same simulations show that the suppression of rain is well described in terms of cloud drop effective radius (re). Rain is initiated when re near cloud top is around 12–14 μm. Cloud water starts to get depleted when column‐maximum rain intensity (Rmax) exceeds 0.1 mm h−1. This happens when cloud‐top re reaches 14 μm. Rmax is mostly less than 0.1 mm h−1 at re < 14 μm, regardless of the cloud water path, but increases rapidly when re exceeds 14 μm. This is in agreement with recent aircraft observations and theoretical studies in convective clouds so that the mechanism is not limited to describing marine stratocumulus. These results support the hypothesis that the onset of significant precipitation is determined by the number of nucleated cloud drops and the depth (D) above cloud base within the cloud that is required for cloud drops to reach re of 14 μm. In turn, this can explain the conditions for initiation of significant drizzle and opening of closed cells providing the basis for a simple parameterization for GCMs that unifies the representation of both precipitating and non‐precipitating clouds as well as the transition between them. Furthermore, satellite global observations of cloud depth (from base to top), and cloud‐top re can be used to derive and validate this parameterization.
Proteomic Study of Low-Temperature Responses in Strawberry Cultivars (Fragaria×ananassa) That Differ in Cold Tolerance
Authors: Koehler Gage , Wilson Robert C. , Goodpaster John V. , Sønsteby Anita , Lai Xianyin , Witzmann Frank A. , You Jin-Sam , Rohloff Jens , Randall Stephen K. , Alsheikh Muath 
Published: June 2012

AbstractTo gain insight into the molecular basis contributing to overwintering hardiness, a comprehensive proteomic analysis comparing crowns of octoploid strawberry (Fragaria × ananassa) cultivars that differ in freezing tolerance was conducted. Four cultivars were examined for freeze tolerance and the most cold-tolerant cultivar (‘Jonsok’) and least-tolerant cultivar (‘Frida’) were compared with a goal to reveal how freezing tolerance is achieved in this distinctive overwintering structure and to identify potential cold-tolerance-associated biomarkers. Supported by univariate and multivariate analysis, a total of 63 spots from two-dimensional electrophoresis analysis and 135 proteins from label-free quantitative proteomics were identified as significantly differentially expressed in crown tissue from the two strawberry cultivars exposed to 0-, 2-, and 42-d cold treatment. Proteins identified as cold-tolerance-associated included molecular chaperones, antioxidants/detoxifying enzymes, metabolic enzymes, pathogenesis-related proteins, and flavonoid pathway proteins. A number of proteins were newly identified as associated with cold tolerance. Distinctive mechanisms for cold tolerance were characterized for two cultivars. In particular, the ‘Frida’ cold response emphasized proteins specific to flavonoid biosynthesis, while the more freezing-tolerant ‘Jonsok’ had a more comprehensive suite of known stress-responsive proteins including those involved in antioxidation, detoxification, and disease resistance. The molecular basis for ‘Jonsok’-enhanced cold tolerance can be explained by the constitutive level of a number of proteins that provide a physiological stress-tolerant poise.
Polymorphisms of pro‐inflammatory cytokine genes and the risk for acute suppurative or chronic nonsuppurative apical periodontitis in a Colombian population
Authors: Amaya M. P. , Criado L. , Blanco B. , Gómez M. , Torres O. , Flórez L. , González C. I. , Flórez O. 
Published: June 2012

AbstractAimTo determine the association of functional single nucleotide polymorphisms in genes of the pro‐inflammatory cytokines tumour necrosis factor‐α, interleukin‐1β, interleukin‐8 and interleukin‐12B with the development of two clinical forms of apical periodontitis (AP): acute suppurative and chronic nonsuppurative.MethodologyThe study included 120 patients from Bucaramanga City, Colombia, 63 diagnosed with acute suppurative AP (ASAP) and 57 diagnosed with chronic nonsuppurative AP (CNAP). Genotyping for
IL1B
+3954 (rs1143634),
IL8
/
CXCL8
−251 (rs4073),
IL12B
+1188 (rs3212227) and
TNFA
−308 (rs1800629) was performed by the PCR–restriction fragment length polymorphisms method. The statistical analysis was performed using STATA 10.0 and PLINK V1.07 software.ResultsSignificant differences in the distribution of
IL8
/
CXCL8
−251 A allele (P adjusted = 0.041; OR adjusted = 0.41, CI adjusted = 0.31–0.97) and
IL8
/
CXCL
−251 TT genotype (P adjusted = 0.04; OR adjusted = 2.24, CI adjusted = 1.04–4.84) were observed comparing patients diagnosed with ASAP and CNAP. No association was observed in genotype and allele distribution for other genetic polymorphisms analysed.ConclusionThis study provides molecular epidemiological evidence that suggests in the present cohort that
IL8
/
CXCL8
−251 T allele, which is associated with higher production of IL8/CXCL8, is also associated with a higher risk of developing acute suppurative form of AP, whereas
IL8
/
CXCL8
−251 A allele, which is associated with lower production of IL8/CXCL8, is associated with chronic nonsuppurative form of AP. This suggests a pivotal role for IL‐8/CXCL8 in periapical disease because of its ability to induce chemotaxis and modulating the directed migration of neutrophils to the site of inflammation in response to microbial infection of pulp.
An observational study of hand hygiene compliance in paediatric wards
Authors: Randle Jacqueline , Firth Joseph , Vaughan Natalie 
Published: June 2012

Aims and objectives.  To measure healthcare workers’, children’s and visitors’ hand hygiene compliance in a paediatric oncology ward and a paediatric respiratory ward in an English hospital.Background.  Children are especially vulnerable to healthcare‐associated infections, yet few studies have reported on hand hygiene compliance in paediatric clinical areas.Design.  This was an observational study.Method.  We measured hand hygiene compliance over an eight‐hour period in two hospital wards using the ‘five moments of hand hygiene’ observation tool. We monitored a total of 407 hand hygiene opportunities.Results.  Overall opportunities for compliance were 74% for healthcare workers (n = 315) and children and visitors 23% (n = 92). Compliance was 84% for allied health professionals, 81% for doctors, 75% for nurses and 73% for ancillary and other staff. Hand hygiene compliance varied depending on which of the five moments of hygiene healthcare workers were undertaking (p < 0·001), with compliance before child contact 90% (140/155); after child contact 78% (89/114); after body fluid exposure 75% (3/4); and after surroundings contact 36% (15/42). For healthcare workers and visitors, there was no evidence of an association between time of day and their hand hygiene compliance, and for visitors to the oncology ward, hand hygiene compliance was higher (p < 0·05).Conclusion.  Owing to the nature of the clinical environments, we are unable to draw conclusions about children’s hand hygiene compliance; however, visitors’ compliance was low. Among healthcare workers, levels of compliance were higher compared with previous reported estimates.Relevance to clinical practice.  Visitors had the lowest level of compliance yet owing to the nature of the clinical environments, nearly a quarter of care is delivered by them rather than healthcare workers, and so, this offers opportunities for specific future interventions aimed at families and carers.
Changes in intern attitudes toward medical error and disclosure
Authors: Varjavand Nielufar , Bachegowda Lohith S , Gracely Edward , Novack Dennis H 
Published: June 2012

Medical Education 2012: 46:668–677Context  The 2000 Institute of Medicine report, ‘To Err is Human: Building a Safer Health System’, focused the medical community on medical error. This focus led to educational initiatives and legislation designed to minimise errors and increase their disclosure.Objectives  This study aimed to investigate whether increased general awareness about medical error has affected interns’ attitudes toward medical error and disclosure by comparing responses to surveys of interns carried out at either end of the last decade.Methods  Two cohorts of interns for the academic years 1999, 2000 and 2001 (n = 304) and 2008 and 2009 (n = 206) at a university hospital were presented with two hypothetical scenarios involving errors that resulted in, respectively, no permanent harm and an adverse outcome. The interns were questioned regarding their likely responses to error and disclosure.Results  We collected 510 surveys (100% response rate). For both scenarios, the percentage of interns who would be willing to fully disclose their mistakes increased substantially from 1999–2001 to 2008–2009 (‘no permanent harm’: 38% and 71%, respectively [p < 0.001]; ‘adverse outcome’: 29% and 55%, respectively [p < 0.001]). About two thirds of fully disclosing interns in both scenarios believed ‘the patient’s right to full information’ to be the primary reason for their disclosure. Fear of litigation in response to error disclosure decreased (70% and 52%, respectively), the percentage of interns who felt that ‘medical mistakes are preventable if doctors know enough’ decreased (49% and 31%, respectively), belief that competent doctors keep emotions and uncertainties to themselves decreased (51% and 14%, respectively), and agreement with leaving medicine if one (as an intern) caused harm or death decreased (50% and 3%, respectively). Prior training about medical mistakes increased more than four‐fold between the cohorts.Conclusions  This comparison of intern responses to a survey administered at either end of the last decade reveals that there may have been some important changes in interns’ intended disclosure practices and attitudes toward medical error.
Relationship between clinical experiences and internal medicine clerkship performance
Authors: Dong Ting , Artino Anthony R , Durning Steven J , Denton Gerald D 
Published: June 2012

Medical Education 2012: 46:689–697Objectives  This study was conducted to assess the associations between several clerkship process measures and students’ clinical and examination performance in an internal medicine clerkship.Methods  We collected data from the internal medicine clerkship at one institution over a 3‐year period (classes of 2010–2012; n = 507) and conducted correlation and multiple regression analyses. We examined the associations between clerkship process measures (student‐reported number of patients evaluated, percentage of core problems encountered, total number of core problems encountered, total number of clinics attended) and four clerkship outcomes (clinical points [a weighted summation of a student’s clinical grade recommendations], ambulatory clinical points [the out‐patient portion of clinical points], examination points [a weighted summation of scores on three clerkship examinations], and National Board of Medical Examiners examination score).Results  After controlling for pre‐clerkship ability and gender, percentage of core problems was significantly associated with ambulatory clinical points (b = 3.84, total model R2 = 0.14). Further, number of patients evaluated was significantly associated with clinical points (b = 0.19, total model R2 = 0.22), but only for students who undertook first‐quarter clerkships, who reported higher numbers of patients.Conclusions  Notwithstanding a few positive (but small) associations, the results from this study suggest that clinical exposure is, at best, weakly associated with internal medicine clerkship performance.