bluuebunny/crossref_metadata_2025 huggingface dataset:
Maximization, learning, and economic behavior
Authors: Erev Ido , Roth Alvin E.
Published: July 2014

The rationality assumption that underlies mainstream economic theory has proved to be a useful approximation, despite the fact that systematic violations to its predictions can be found. That is, the assumption of rational behavior is useful in understanding the ways in which many successful economic institutions function, although it is also true that actual human behavior falls systematically short of perfect rationality. We consider a possible explanation of this apparent inconsistency, suggesting that mechanisms that rest on the rationality assumption are likely to be successful when they create an environment in which the behavior they try to facilitate leads to the best payoff for all agents on average, and most of the time. Review of basic learning research suggests that, under these conditions, people quickly learn to maximize expected return. This review also shows that there are many situations in which experience does not increase maximization. In many cases, experience leads people to underweight rare events. In addition, the current paper suggests that it is convenient to distinguish between two behavioral approaches to improve economic analyses. The first, and more conventional approach among behavioral economists and psychologists interested in judgment and decision making, highlights violations of the rational model and proposes descriptive models that capture these violations. The second approach studies human learning to clarify the conditions under which people quickly learn to maximize expected return. The current review highlights one set of conditions of this type and shows how the understanding of these conditions can facilitate market design.
Human (Clovis)–gomphothere (Cuvieroniussp.) association ∼13,390 calibrated yBP in Sonora, Mexico
Authors: Sanchez Guadalupe , Holliday Vance T. , Gaines Edmund P. , Arroyo-Cabrales Joaquín , Martínez-Tagüeña Natalia , Kowler Andrew , Lange Todd , Hodgins Gregory W. L. , Mentzer Susan M. , Sanchez-Morales Ismael
Published: July 2014

Significance

Archaeological evidence from Sonora, Mexico, indicates that the earliest widespread and recognizable group of hunter-gatherers (“Clovis”) were in place ∼13,390 y ago in southwestern North America. This is the earliest well-documented population on the continent and suggests that the unique Clovis artifact style originated in the southwest or south central part of the continent, well south of the Arctic gateways into the continent. These hunters targeted gomphotheres, an elephant common in south and central North America, but unknown in association with humans or at this late age in North America.
Neural correlates of dueling affective reactions to win–win choices
Authors: Shenhav Amitai , Buckner Randy L.
Published: July 2014

Significance

Choices between multiple good prospects (e.g., job offers) are known to generate anxiety, even as the decision maker feels positivity toward their options. Here, we explored the basis for these (paradoxically) simultaneously occurring experiences. We evaluated brain activity during win–win choices relative to how positive and anxious the participant later reported having felt when encountering a set of options, and relative to subsequent choice reversals. Our participants felt increasingly positive and anxious with increasingly good options, and these two experiences were accounted for by dissociable neural circuits. Positivity-related circuits primarily tracked the value of the best item whereas anxiety-related circuits primarily tracked the level of competition between potential responses, and whether the participants would later decide to reverse their choice.
In situ studies of a platform for metastable inorganic crystal growth and materials discovery
Authors: Shoemaker Daniel P. , Hu Yung-Jin , Chung Duck Young , Halder Gregory J. , Chupas Peter J. , Soderholm L. , Mitchell J. F. , Kanatzidis Mercouri G.
Published: July 2014

Significance

Dense inorganic materials comprise most functional electronic, optical, and magnetic devices. Whereas the discovery of new inorganic materials can increase our technical capabilities and uncover new phenomena, the search is difficult due to their formation at high temperatures where only the most stable (often known) materials can be isolated postreaction. We find a variety of unexpected and unknown materials nucleating at moderate temperatures in molten salts. By probing these processes with in situ diffraction, we are able to identify a large variety of new phases quickly and pave a path to more efficient materials discovery.
Recent evolution of equine influenza and the origin of canine influenza
Authors: Collins Patrick J. , Vachieri Sebastien G. , Haire Lesley F. , Ogrodowicz Roksana W. , Martin Stephen R. , Walker Philip A. , Xiong Xiaoli , Gamblin Steven J. , Skehel John J.
Published: July 2014

Significance

Equine influenza viruses of the H3N8 subtype have caused outbreaks of respiratory disease in horses throughout the world since their discovery in 1963 in Florida. In 2004 an equine virus in circulation was transmitted to dogs and subsequently spread throughout the United States and to Europe. Comparative analyses of the structures of hemagglutinin glycoproteins of equine and canine viruses by X-ray crystallography locate the sites of variation on the molecules, indicate a role in determining binding specificity for an amino acid sequence difference in the receptor binding site, and describe a unique structural difference in the membrane fusion region in recent equine and canine virus HAs by comparison with all other known HAs. These differences are proposed to have facilitated cross-species transfer.
Paradoxical thinking as a new avenue of intervention to promote peace
Authors: Hameiri Boaz , Porat Roni , Bar-Tal Daniel , Bieler Atara , Halperin Eran
Published: July 2014

Significance

The premise of most interventions that aim to promote peacemaking is that information that is inconsistent with held beliefs causes tension, which may motivate alternative information seeking. However, individuals—especially during conflict—use different defenses to preserve their societal beliefs. Therefore, we developed a new paradoxical thinking intervention that provides consistent—though extreme—information, with the intention of raising a sense of absurdity but not defenses. We examined our hypotheses in a longitudinal field experiment and found that participants who were exposed to the intervention expressed more conciliatory attitudes regarding the conflict, even 1 y after the intervention, which also manifested in their voting (self-report measure) to more dovish parties in the Israeli 2013 elections.
Platelets guide the formation of early metastatic niches
Authors: Labelle Myriam , Begum Shahinoor , Hynes Richard O.
Published: July 2014

Significance

Specialized microenvironments (or “niches”) are essential for metastasis, but how cancer cells and host cells contribute to their establishment remains poorly understood. Our study reveals that platelets and granulocytes are sequentially recruited to disseminated tumor cells to form “early metastatic niches” that promote metastatic progression. Importantly, the recruitment of granulocytes is not primarily due to tumor cell-derived signals but rather relies on platelet-derived CXCL5/7 chemokines. Prevention of granulocyte recruitment via inhibition of the CXCL5/7 receptor CXCR2, or depletion of either platelets or granulocytes inhibits metastasis, thereby uncovering a key role for platelet-to-granulocyte signaling in the establishment of metastases. Specific inhibition of platelet-to-granulocyte interactions may thus represent a valuable antimetastatic therapy in addition to cancer cell-centered treatments.
Copy number alteration burden predicts prostate cancer relapse
Authors: Hieronymus Haley , Schultz Nikolaus , Gopalan Anuradha , Carver Brett S. , Chang Matthew T. , Xiao Yonghong , Heguy Adriana , Huberman Kety , Bernstein Melanie , Assel Melissa , Murali Rajmohan , Vickers Andrew , Scardino Peter T. , Sander Chris , Reuter Victor , Taylor Barry S. , Sawyers Charles L.
Published: July 2014

Significance

Prostate cancer is a major health burden with significant overtreatment because of difficulty segregating high- and low-risk disease. Discovery of biomarkers that stratify risk could have a broad public health impact but requires cohorts with comprehensive molecular and clinical follow-up. We characterize two independent prostate cancer cohorts with genomic and clinical data that include biochemical recurrence and metastasis. We demonstrate that copy number alteration (CNA) burden, a measure of the fraction of a tumor genome that is copy number altered, is prognostic for recurrence and metastasis. CNA burden is also associated with cancer recurrence in an intermediate risk population, and can be identified in biopsies. This work provides a clinicogenomic resource and highlights oncogenomics' potential to identify needed prognostic factors.
Stromal response to Hedgehog signaling restrains pancreatic cancer progression
Authors: Lee John J. , Perera Rushika M. , Wang Huaijun , Wu Dai-Chen , Liu X. Shawn , Han Shiwei , Fitamant Julien , Jones Phillip D. , Ghanta Krishna S. , Kawano Sally , Nagle Julia M. , Deshpande Vikram , Boucher Yves , Kato Tomoyo , Chen James K. , Willmann Jürgen K. , Bardeesy Nabeel , Beachy Philip A.
Published: July 2014

Significance

Preclinical studies have suggested that Hedgehog (Hh) pathway inhibition reduces growth and metastasis of pancreatic ductal adenocarcinoma (PDA), but ensuing clinical trials of Hh pathway antagonists combined with cytotoxic chemotherapy have not succeeded. Here, we find in three distinct genetically engineered mouse models that genetic and pharmacologic inhibition of Hh pathway activity actually accelerates PDA progression. Furthermore, we find that the acute modulation of pathway activity regulates the balance between epithelial and stromal elements, with inhibition causing suppression of desmoplasia and accelerated growth of epithelial elements and activation causing stromal hyperplasia and reduced growth of the neoplastic epithelium. Our study explains previous clinical trial results and suggests the possibility of novel types of therapeutic interventions.
Chapter 1.2 Dimensions of register variation in Brazilian Portuguese
Authors: Berber Sardinha Tony , Kauffmann Carlos , Acunzo Cristina Mayer
Published: July 2014

In this chapter, we present an MD analysis of Brazilian Portuguese, based on the Brazilian Register Variation Corpus, comprising 48 different spoken and written registers. The previous literature on text varieties in Brazilian Portuguese focuses on specific aspects of one or at most a few varieties at a time and, therefore, does not present a comprehensive picture of register use in Brazilian Portuguese. In this study, we attempt to fill this gap by employing the MD framework, which enabled us to account for a large number of different registers, based on a wide range of linguistic features. The analysis revealed six dimensions of variation, which are presented and discussed in this chapter.
Chapter 1.3 25 years later
Authors: Berber Sardinha Tony
Published: July 2014

This chapter presents a study aimed at comparing Internet and pre-Internet text varieties along the dimensions of register variation introduced by Biber (1988). The research uses the recommendations for corpus design set forth by Biber (1993) for the compilation of a representative corpus of online communication, containing texts from webpages, blogs, emails, and Twitter and Facebook messages. The multi-dimensional analysis performed is additive, whereby the dimension scores for the Internet registers are mapped on the existing multidimensional space from Biber (1988). The results indicate that Internet registers share considerable linguistic similarities with registers from the pre-Internet era, yet they also have particular characteristics that set them apart from their extant counterparts. The chapter details these similarities and differences.
Chapter 2.1 Dimensions of variation in North American movies
Authors: Veirano Pinto Marcia
Published: July 2014

This chapter investigates variation in the verbal language of 640 North American movies released between 1930 and 2010, taking into account situational variables such as movie genres, year of release in the United States, public and critic ratings, movie length, directors, movie studios, nature of the script (original/adapted), as well as awards/nominations received. A Multi-Dimensional analysis proposes seven dimensions of variation for the register and uses the identified situational variables to partially explain the variation found within the register across the years. The results indicated that movie genres, year of release, movie length, nature of the script, and awards/nominations received are the variables that account for the variation observed.
Chapter 2.2 Multi-Dimensional analysis of pop songs
Authors: Bértoli-Dutra Patrícia
Published: July 2014

This chapter reports on an MD analysis of North American and British pop songs from 1940 to 2009, comprising 6,290 individual songs from 32 artists and bands, representing 16 different music styles or genres. The corpus was automatically tagged for part of speech and semantic field. In addition, multi-word units in each song were identified and checked both against the Google 1 trillion word 3-gram corpus and against the whole song corpus in order to measure the use of formulaic language. The principal component analysis showed two sets of three factors, one for lexico-grammar and one for semantics. These were interpreted as dimensions, and the most representative songs, artists, styles, and time periods for each dimension were identified. Overall, this study advocates the relevance of song lyrics as an object of linguistic investigation.
Chapter 2.3 Dimensions of variation in TIME magazine
Authors: de Souza Renata Condi
Published: July 2014

This chapter presents an analysis of TIME magazine cover stories published between 1923 and 2011. This research applies the Multi-Dimensional framework in two ways: by adding the TIME magazine texts to the five main dimensions of variation defined by Biber (1988) and by extracting the dimensions of variation that are specific to the magazine using a new factor analysis. The chapter also reports on the assessment of the role of external factors on the variation, including editorial changes, and the political, economic, and military events during which the texts were published. Finally, the chapter reveals the text types (i.e. linguistically defined varieties) present in TIME magazine.
Giving it my best shot
Authors: Tucker Gordon H.
Published: July 2014

In this article I explore the extent to which the analysis of metaphoricallyderivedexpressions, such as “give someone a hug”, differs from that assigned tothe prototypical sense associated with the main verb in question. Taking expressionsinvolving the verb “give”, I consider a range of semantic departures fromprototypical “give”, in respect of the process type (material, mental, relationalprocess etc.) and the participant roles present. Using a Systemic FunctionalGrammar framework, I analyse candidate expressions according to their lexicogrammaticalpotential (e.g. associated syntactic alternation potential) and aset of tests to establish the participant roles present. The results of the analysisindicate a cline of differing degrees of lexicogrammatical departure from theprototype, reflecting their respective semantic departure.
The cultural classification of ‘things’
Authors: Fawcett Robin P.
Published: July 2014

We begin by distinguishing between an ontology and a semantic system networkfor noun senses. i.e. a cultural classification of ‘things’. Next, we locate this ina systemic functional lexicogrammar, and evaluate two ways of representingit. Then we explore: (i) the reason for its overall structure; (ii) the central roleof probabilities; (iii) how to model the [mass] v [count] distinction (and twoothers; (iv) two crucial non-taxonomic relationships; (v) three types of non-experientialmeaning; and (vi) the key role of realization rules in generatingnouns as heads of nominal groups. With nearly 5,000 noun senses, the CardiffGrammar’s network for the cultural classification of “things” is probably thelargest in existence. Yet it needs further development, and readers are invitedboth to use this valuable resource and to help expand it.
Modification as a propositional act
Authors: Rijkhoff Jan
Published: July 2014

A complete functional theory of grammar should be able to specify the communicative
function of each constituent in a sentence (or rather ‘Discourse
Act’). Whereas predicating and referring have been given due attention
in functional approaches to grammar, the modifying function of linguistic
material in a Discourse Act has been largely ignored. This chapter argues (i) that
modifying is no less actional than predicating or referring in the process of verbal
communication and (ii) that the modifying function of linguistic material
should be specified at the highest level of representation in Functional Discourse
Grammar. Apart from Attitudinal Modification, there are at least five Subacts
of Modification that are required for an adequate functional analysis of noun
phrases and clauses: classifying modification, qualifying modification,
quantifying modification, localizing modification and discoursereferential
modification.
Derivational morphology in Functional Discourse Grammar
Authors: García Velasco Daniel , Keizer Evelien
Published: July 2014

The aim of this paper is to provide a general overview of derivational morphology
in Functional Discourse Grammar (FDG) as presented in Hengeveld and
Mackenzie (2008). The paper begins with a brief description of the model with
special reference to those properties which are relevant in the characterization
of derivational processes; it also discusses the differences between classical
Functional Grammar (FG) and the current FDG model. It is argued that two
novel features of FDG are of special relevance: the separation of frames and lexemes,
which entails that the Predicate Formation Rules employed in FG are no
longer an option, and the distinction between Lexemes at the Representational
Level and Words at the Morphosyntactic Level, with the consequence that morphological
processes have impact on various levels of representation. Finally,
some examples of key derivational processes (compounding, affixation, and
valency changing operations) are provided to show how these processes can be
handled in the model.
"Agreement" as a perspectivizing device in discourse
Authors: Cornish Francis
Published: July 2014

The description of agreement brings into play a number of different components
and levels of analysis. This chapter’s goal is to show how stating certain
agreement facts requires reference to each of the levels and components available
within the Functional Discourse Grammar model. Agreement’s raison
d’être in discourse concerns the (re)identification and establishment of referents.
Its manifestation depends on the assumed properties of the intended referent
as conceptualised by users, as well as on what is being predicated of it. Thus
agreement is not purely redundant, semantically empty and grammatically
predictable (as is often claimed), but may perform several key functions at the
level of discourse, the chief one of which is the superimposition of a referential
perspective on the intended referent.
Interfacing the lexicon and an ontology in a linking system
Authors: Van Valin Jr. Robert D. , Mairal-Usón Ricardo
Published: July 2014

The aim of this paper is to discuss the repercussions of a conceptual orientation
on two crucial parts of the Role and Reference Grammar (RRG) linking
algorithm, that is, semantic representation and constructional schemas. Firstly,
it is argued that adopting FunGramKB’s notion of conceptual logical structure
(CLS) over standard RRG logical structures (LSs) has numerous advantages
since meaning has now access to conceptual knowledge and therefore a CLS
provides a format that goes beyond those aspects that are syntactically visible.
The second part introduces the notion of the grammaticon, the component
where constructional schemas actually reside. RRG constructional schemas are
analyzed within a conceptual framework like that provided in FunGramKB. In
essence, it is shown that a conceptual orientation to the RRG linking system by
the addition of CLSs enriches the semantic representations in it substantially.
Cognitive functionalism in language education
Authors: Hudson Richard A.
Published: July 2014

Functional pressures on language are always cognitive, and cognitive pressuresare always functional, so cognitivism and functionalism combine to explain thestructure of lexicogrammar – the continuum of lexicon and grammar – andalso the statistics of language usage. As an example, the paper shows how WordGrammar explains the difficulty of centre-embedding in terms of dependencysyntax combined with a general cognitive principle of binding, and also thebenefits of non-canonical word orders (such as extraposition) in the lexicogrammar.These reordering options are part of the formal academic languagethat children learn through education, and education should be guided bylinguistic research. This is a research area that calls for far more effort and collaborationwith other disciplines.
DNA damage-specific deubiquitination regulates Rad18 functions to suppress mutagenesis
Authors: Zeman Michelle K. , Lin Jia-Ren , Freire Raimundo , Cimprich Karlene A.
Published: July 2014

Deoxyribonucleic acid (DNA) lesions encountered during replication are often bypassed using DNA damage tolerance (DDT) pathways to avoid prolonged fork stalling and allow for completion of DNA replication. Rad18 is a central E3 ubiquitin ligase in DDT, which exists in a monoubiquitinated (Rad18•Ub) and nonubiquitinated form in human cells. We find that Rad18 is deubiquitinated when cells are treated with methyl methanesulfonate or hydrogen peroxide. The ubiquitinated form of Rad18 does not interact with SNF2 histone linker plant homeodomain RING helicase (SHPRH) or helicase-like transcription factor, two downstream E3 ligases needed to carry out error-free bypass of DNA lesions. Instead, it interacts preferentially with the zinc finger domain of another, nonubiquitinated Rad18 and may inhibit Rad18 function in trans. Ubiquitination also prevents Rad18 from localizing to sites of DNA damage, inducing proliferating cell nuclear antigen monoubiquitination, and suppressing mutagenesis. These data reveal a new role for monoubiquitination in controlling Rad18 function and suggest that damage-specific deubiquitination promotes a switch from Rad18•Ub–Rad18 complexes to the Rad18–SHPRH complexes necessary for error-free lesion bypass in cells.
The conserved potassium channel filter can have distinct ion binding profiles: Structural analysis of rubidium, cesium, and barium binding in NaK2K
Authors: Lam Yee Ling , Zeng Weizhong , Sauer David Bryant , Jiang Youxing
Published: July 2014

Potassium channels are highly selective for K+ over the smaller Na+. Intriguingly, they are permeable to larger monovalent cations such as Rb+ and Cs+ but are specifically blocked by the similarly sized Ba2+. In this study, we used structural analysis to determine the binding profiles for these permeant and blocking ions in the selectivity filter of the potassium-selective NaK channel mutant NaK2K and also performed permeation experiments using single-channel recordings. Our data revealed that some ion binding properties of NaK2K are distinct from those of the canonical K+ channels KcsA and MthK. Rb+ bound at sites 1, 3, and 4 in NaK2K, as it does in KcsA. Cs+, however, bound predominantly at sites 1 and 3 in NaK2K, whereas it binds at sites 1, 3, and 4 in KcsA. Moreover, Ba2+ binding in NaK2K was distinct from that which has been observed in KcsA and MthK, even though all of these channels show similar Ba2+ block. In the presence of K+, Ba2+ bound to the NaK2K channel at site 3 in conjunction with a K+ at site 1; this led to a prolonged block of the channel (the external K+-dependent Ba2+ lock-in state). In the absence of K+, however, Ba2+ acts as a permeating blocker. We found that, under these conditions, Ba2+ bound at sites 1 or 0 as well as site 3, allowing it to enter the filter from the intracellular side and exit from the extracellular side. The difference in the Ba2+ binding profile in the presence and absence of K+ thus provides a structural explanation for the short and prolonged Ba2+ block observed in NaK2K.
Disrupted coupling of gating charge displacement to Na+ current activation for DIIS4 mutations in hypokalemic periodic paralysis
Authors: Mi Wentao , Rybalchenko Volodymyr , Cannon Stephen C.
Published: July 2014

Missense mutations at arginine residues in the S4 voltage-sensor domains of NaV1.4 are an established cause of hypokalemic periodic paralysis, an inherited disorder of skeletal muscle involving recurrent episodes of weakness in conjunction with low serum K+. Expression studies in oocytes have revealed anomalous, hyperpolarization-activated gating pore currents in mutant channels. This aberrant gating pore conductance creates a small inward current at the resting potential that is thought to contribute to susceptibility to depolarization in low K+ during attacks of weakness. A critical component of this hypothesis is the magnitude of the gating pore conductance relative to other conductances that are active at the resting potential in mammalian muscle: large enough to favor episodes of paradoxical depolarization in low K+, yet not so large as to permanently depolarize the fiber. To improve the estimate of the specific conductance for the gating pore in affected muscle, we sequentially measured Na+ current through the channel pore, gating pore current, and gating charge displacement in oocytes expressing R669H, R672G, or wild-type NaV1.4 channels. The relative conductance of the gating pore to that of the pore domain pathway for Na+ was 0.03%, which implies a specific conductance in muscle from heterozygous patients of ∼10 µS/cm2 or 1% of the total resting conductance.

Unexpectedly, our data also revealed a substantial decoupling between gating charge displacement and peak Na+ current for both R669H and R672G mutant channels. This decoupling predicts a reduced Na+ current density in affected muscle, consistent with the observations that the maximal dV/dt and peak amplitude of the action potential are reduced in fibers from patients with R672G and in a knock-in mouse model of R669H. The defective coupling between gating charge displacement and channel activation identifies a previously unappreciated mechanism that contributes to the reduced excitability of affected fibers seen with these mutations and possibly with other R/X mutations of S4 of NaV, CaV, and KV channels associated with human disease.
Congenital Heart Disease and Pulmonary Arterial Hypertension in South America (2013 Grover Conference Series)
Authors: Lopes Antonio Augusto , Flores Patricia C. , Diaz Gabriel F. , Mesquita Sonia M. F.
Published: July 2014

South America is a territory of 17,819,100 km2, where ∼388 million people live in 13 countries. In the region, access to medical assistance (e.g., for treatment of cardiovascular disorders) is relatively easy in metropolitan areas but difficult in remote places such as the Andes and the Amazon. Altitudes up to ∼6,700 m influence the prevalence of congenital heart disease (CHD) and pulmonary arterial hypertension (PAH). In tertiary centers, CHD is now treated earlier in life but remains an important etiology of PAH. In adolescents and adults with PAH assisted at institutions devoted to treatment of cardiovascular disorders, the relative frequency of PAH‐CHD (∼50%–60%) is even higher than that of idiopathic PAH. In one big tertiary center in São Paulo, Brazil, the prevalence of advanced PAH in children and adults with CHD is 1.2% and 4.2%, respectively. In young patients with cardiac septal defects (aged up to 2 years), pulmonary vascular abnormalities are a matter of concern in the decision about operability in 4.9% of cases. Access to specific PAH drugs is not uniform in South America, being unrealistic in remote places. In big cities, there are real possibilities for management of complex CHD, neonatal disorders, and even cardiac transplantation. Research activities have been implemented at clinical, translational, and basic levels. However, because of social and economic inequalities and political issues, access to best standards of medical care remains a problem in the region as a whole.
Strategies to Prevent Ventilator-Associated Pneumonia in Acute Care Hospitals: 2014 Update
Authors: Klompas Michael , Branson Richard , Eichenwald Eric C. , Greene Linda R. , Howell Michael D. , Lee Grace , Magill Shelley S. , Maragakis Lisa L. , Priebe Gregory P. , Speck Kathleen , Yokoe Deborah S. , Berenholtz Sean M.
Published: July 2014

Previously published guidelines are available that provide comprehensive recommendations for detecting and preventing healthcare-associated infections (HAIs). The intent of this document is to highlight practical recommendations in a concise format to assist acute care hospitals in implementing and prioritizing strategies to prevent ventilator-associated pneumonia (VAP) and other ventilator-associated events (VAEs) and to improve outcomes for mechanically ventilated adults, children, and neonates. This document updates "Strategies to Prevent Ventilator-Associated Pneumonia in Acute Care Hospitals," published in 2008. This expert guidance document is sponsored by the Society for Healthcare Epidemiology of America (SHEA) and is the product of a collaborative effort led by SHEA, the Infectious Diseases Society of America (IDSA), the American Hospital Association (AHA), the Association for Professionals in Infection Control and Epidemiology (APIC), and The Joint Commission, with major contributions from representatives of a number of organizations and societies with content expertise. The list of endorsing and supporting organizations is presented in the introduction to the 2014 updates.
Strategies to Prevent Healthcare-Associated Infections through Hand Hygiene
Authors: Ellingson Katherine , Haas Janet P. , Aiello Allison E. , Kusek Linda , Maragakis Lisa L. , Olmsted Russell N. , Perencevich Eli , Polgreen Philip M. , Schweizer Marin L. , Trexler Polly , VanAmringe Margaret , Yokoe Deborah S.
Published: July 2014

Previously published guidelines provide comprehensive recommendations for hand hygiene in healthcare facilities. The intent of this document is to highlight practical recommendations in a concise format, update recommendations with the most current scientific evidence, and elucidate topics that warrant clarification or more robust research. Additionally, this document is designed to assist healthcare facilities in implementing hand hygiene adherence improvement programs, including efforts to optimize hand hygiene product use, monitor and report back hand hygiene adherence data, and promote behavior change. This expert guidance document is sponsored by the Society for Healthcare Epidemiology of America (SHEA) and is the product of a collaborative effort led by SHEA, the Infectious Diseases Society of America (IDSA), the American Hospital Association (AHA), the Association for Professionals in Infection Control and Epidemiology (APIC), and The Joint Commission, with major contributions from representatives of a number of organizations and societies with content expertise. The list of endorsing and supporting organizations is presented in the introduction to the 2014 updates.
An improved method for computing q-values when the distribution of effect sizes is asymmetric
Authors: Orr Megan , Liu Peng , Nettleton Dan
Published: July 2014

Motivation : Asymmetry is frequently observed in the empirical distribution of test statistics that results from the analysis of gene expression experiments. This asymmetry indicates an asymmetry in the distribution of effect sizes. A common method for identifying differentially expressed (DE) genes in a gene expression experiment while controlling false discovery rate (FDR) is Storey’s q -value method. This method ranks genes based solely on the P -values from each gene in the experiment.

Results: We propose a method that alters and improves upon the q -value method by taking the sign of the test statistics, in addition to the P -values, into account. Through two simulation studies (one involving independent normal data and one involving microarray data), we show that the proposed method, when compared with the traditional q -value method, generally provides a better ranking for genes as well as a higher number of truly DE genes declared to be DE, while still adequately controlling FDR. We illustrate the proposed method by analyzing two microarray datasets, one from an experiment of thale cress seedlings and the other from an experiment of maize leaves.

Availability and implementation : The R code and data files for the proposed method and examples are available at Bioinformatics online.

Contact : megan.orr@ndsu.edu

Supplementary information : Supplementary data are available at Bioinformatics online.
IgG4-related disease and its pathogenesis—cross-talk between innate and acquired immunity
Authors: Umehara Hisanori , Nakajima Akio , Nakamura Takuji , Kawanami Takafumi , Tanaka Masao , Dong Lingli , Kawano Mitsuhiro
Published: July 2014

IgG4-related disease (IgG4-RD) is a novel clinical entity proposed in Japan in the 21th century and is attracting strong attention over the world. The characteristic manifestations of IgG4-RD are increased serum IgG4 concentration and tumefaction by IgG4+ plasma cells. Although the clinical manifestations in various organs have been established, the pathogenesis of IgG4-RD is still unknown. Recently, many reports of aberrant acquired immunity such as Th2-diminated immune responses have been published. However, many questions still remain, including questions about the pathogenesis of IgG4-RD and the roles of IgG4. In this review, we discuss the pathogenesis of IgG4-RD by focusing on the cross-talk between innate and acquired immunity.
The hepatitis B virus-associated tumor microenvironment in hepatocellular carcinoma
Authors: Yang Pengyuan , Markowitz Geoffrey J. , Wang Xiao-Fan
Published: July 2014

In contrast to a majority of cancer types, the initiation of hepatocellular carcinoma (HCC) is intimately associated with a chronically diseased liver tissue, with one of the most prevalent etiological factors being hepatitis B virus (HBV). Transformation of the liver in HBV-associated HCC often follows from or accompanies long-term symptoms of chronic hepatitis, inflammation and cirrhosis, and viral load is a strong predictor for both incidence and progression of HCC. Besides aiding in transformation, HBV plays a crucial role in modulating the accumulation and activation of both cellular components of the microenvironment, such as immune cells and fibroblasts, and non-cellular components of the microenvironment, such as cytokines and growth factors, markedly influencing disease progression and prognosis. This review will explore some of these components and mechanisms to demonstrate both underlying themes and the inherent complexity of these interacting systems in the initiation, progression, and metastasis of HBV-positive HCC.
Abundances in the ejecta of core-collapse supernova remnants G350.1−0.3 and G349.7+0.2
Authors: Yasumi Masato , Nobukawa Masayoshi , Nakashima Shinya , Uchida Hiroyuki , Sugawara Ryusuke , Tsuru Takeshi Go , Tanaka Takaaki , Koyama Katsuji
Published: July 2014

We present Suzaku results of the two Galactic supernova remnants (SNRs) G350.1−0.3 and G349.7+0.2. We find Al and Ni Kα lines from both the SNRs for the first time, in addition to previously detected K-shell lines of Mg, Si, S, Ar, Ca, and Fe. The spectra are well described by two optically thin thermal plasmas: a low-temperature (low-kT) plasma in collisional ionization equilibrium and a high-temperature (high-kT) plasma in non-equilibrium ionization. Since the low-kT plasma has solar metal abundances, it is thought to be of interstellar medium origin. The high-kT plasma has super-solar abundances, hence it is likely to be of ejecta origin. The abundance patterns of the ejecta components are similar to those of core-collapse supernovae with progenitor masses of ∼ 15–25 M⊙ for G350.1−0.3 and ∼ 35–40 M⊙ for G349.7+0.2. We find extremely high abundances of Ni compared to Fe (ZNi/ZFe ∼ 8). Based on the measured column densities between the SNRs and the near sky background, we propose that G350.1−0.3 and G349.7+0.2 are located at distances of 9 ± 3 kpc and 12 ± 5 kpc, respectively. Then the ejecta masses are estimated to be ∼ 13 M⊙ and ∼ 24 M⊙ for G350−0.3 and G349.7+0.2, respectively. These values are consistent with the progenitor masses of ∼ 15–25 M⊙ and ∼ 35–40 M⊙ for G350.1−0.3 and G349.7+0.2, respectively.
Comparative and Functional Analysis of the Widely Occurring Family of Nep1-Like Proteins
Authors: Oome Stan , Van den Ackerveken Guido
Published: July 2014

Nep1-like proteins (NLP) are best known for their cytotoxic activity in dicot plants. NLP are taxonomically widespread among microbes with very different lifestyles. To learn more about this enigmatic protein family, we analyzed more than 500 available NLP protein sequences from fungi, oomycetes, and bacteria. Phylogenetic clustering showed that, besides the previously documented two types, an additional, more divergent, third NLP type could be distinguished. By closely examining the three NLP types, we identified a noncytotoxic subgroup of type 1 NLP (designated type 1a), which have substitutions in amino acids making up a cation-binding pocket that is required for cytotoxicity. Type 2 NLP were found to contain a putative calcium-binding motif, which was shown to be required for cytotoxicity. Members of both type 1 and type 2 NLP were found to possess additional cysteine residues that, based on their predicted proximity, make up potential disulfide bridges that could provide additional stability to these secreted proteins. Type 1 and type 2 NLP, although both cytotoxic to plant cells, differ in their ability to induce necrosis when artificially targeted to different cellular compartments in planta, suggesting they have different mechanisms of cytotoxicity.
β-Aminobutyric Acid (BABA)-Induced Resistance in Arabidopsis thaliana: Link with Iron Homeostasis
Authors: Koen Emmanuel , Trapet Pauline , Brulé Daphnée , Kulik Anna , Klinguer Agnès , Atauri-Miranda Livia , Meunier-Prest Rita , Boni Gilles , Glauser Gaétan , Mauch-Mani Brigitte , Wendehenne David , Besson-Bard Angélique
Published: July 2014

β-Aminobutyric acid (BABA) is a nonprotein amino acid inducing resistance in many different plant species against a wide range of abiotic and biotic stresses. Nevertheless, how BABA primes plant natural defense reactions remains poorly understood. Based on its structure, we hypothesized and confirmed that BABA is able to chelate iron (Fe) in vitro. In vivo, we showed that it led to a transient Fe deficiency response in Arabidopsis thaliana plants exemplified by a reduction of ferritin accumulation and disturbances in the expression of genes related to Fe homeostasis. This response was not correlated to changes in Fe concentrations, suggesting that BABA affects the availability or the distribution of Fe rather than its assimilation. The phenotype of BABA-treated plants was similar to those of plants cultivated in Fe-deficient conditions. A metabolomic analysis indicated that both BABA and Fe deficiency induced the accumulation of common metabolites, including p-coumaroylagmatine, a metabolite previously shown to be synthesized in several plant species facing pathogen attack. Finally, we showed that the protective effect induced by BABA against Botrytis cinerea was mimicked by Fe deficiency. In conclusion, the Fe deficiency response caused by BABA could bring the plant to a defense-ready state, participating in the plant resistance against the pathogens.
Modeling Pathogen DNA Content and Visual Disease Assessment in Seed Tubers to Inform Disease in Potato Progeny Root, Stolon, and Tubers
Authors: Tegg Robert S. , Corkrey Ross , Herdina Herdina , McKay Alan C. , Crump Nigel S. , de Boer Rudolf F. , Wiechel Tonya J. , Wilson Calum R.
Published: July 2014

Measurement of pathogens on seed tubers is essential for informing likelihood of subsequent potato disease. Here we utilized quantitative PCR assessment of pathogen DNA and visual assessment of disease to measure seed tuber inoculum and used this to model development of disease in potato grown in pathogen-free soil. Analysis by recursive partitioning and modeling using receiver operating curves indicated both abundance of Rhizoctonia solani AG3 and Streptomyces scabies DNA, and disease symptoms associated with these pathogens on seed tubers could predict subsequent disease in progeny tubers and for R. solani, stolons. In contrast, abundance of Spongospora subterranea DNA and disease symptoms on seed tubers were not consistently associated with powdery scab in progeny tubers. The relationship between S. subterranea DNA and seed tuber symptoms on root galling was stronger. Symptomless seed tubers that carried high levels of S. subterranea DNA were also associated with greater root galling than those with low pathogen DNA levels. There was a modest association between root galling and powdery scab in progeny tubers. These results highlight the importance of using certified seed tubers, and demonstrate a statistical tool for measuring the impact of seed tuber-borne inoculum.
Risk Factors for Proximal Junctional Kyphosis Associated With Dual-rod Growing-rod Surgery for Early-onset Scoliosis
Authors: Watanabe Kota , Uno Koki , Suzuki Teppei , Kawakami Noriaki , Tsuji Taichi , Yanagida Haruhisa , Ito Manabu , Hirano Toru , Yamazaki Ken , Minami Shohei , Taneichi Hiroshi , Imagama Shiro , Takeshita Katsushi , Yamamoto Takuya , Matsumoto Morio
Published: July 2014

Study Design

A retrospective, multicenter study.

Objective:

To identify risk factors for proximal junctional kyphosis (PJK) when treating early-onset scoliosis (EOS) with dual-rod growing-rod (GR) procedure.

Summary of Background Data:

The risk factors for PJK associated with GR treatment for EOS have not been adequately studied.

Methods:

We evaluated clinical and radiographic results from 88 patients with EOS who underwent dual-rod GR surgery in 12 spine centers in Japan. The mean age at the time of the initial surgery was 6.5±2.2 years (range, 1.5–9.8 y), and the mean follow-up period was 3.9±2.6 years (range, 2.0–12.0 y). Risk factors for PJK were analyzed by binomial multiple logistic regression analysis. The potential factors analyzed were sex, etiology, age, the number of rod-lengthening procedures, coronal and sagittal parameters on radiographs, the type of foundation (pedicle screws or hooks), the uppermost level of the proximal foundation, and the lowermost level of the distal foundation.

Results:

PJK developed in 23 patients (26%); in 19 of these, the proximal foundation became dislodged following PJK. Binomial multiple logistic regression analysis identified the following significant independent risk factors for PJK: a lower instrumented vertebra at or cranial to L3 [odds ratio (OR), 3.32], a proximal thoracic scoliosis of ≥40 degrees (OR, 2.95), and a main thoracic kyphosis of ≥60 degrees (OR, 5.08).

Conclusions:

The significant independent risk factors for PJK during dual-rod GR treatment for EOS were a lower instrumented vertebra at or cranial to L3, a proximal thoracic scoliosis of ≥40 degrees, and a main thoracic kyphosis of ≥60 degrees.
High-order computational fluid dynamics tools for aircraft design
Authors: Wang Z. J.
Published: July 2014

Most forecasts predict an annual airline traffic growth rate between 4.5 and 5% in the foreseeable future. To sustain that growth, the environmental impact of aircraft cannot be ignored. Future aircraft must have much better fuel economy, dramatically less greenhouse gas emissions and noise, in addition to better performance. Many technical breakthroughs must take place to achieve the aggressive environmental goals set up by governments in North America and Europe. One of these breakthroughs will be physics-based, highly accurate and efficient computational fluid dynamics and aeroacoustics tools capable of predicting complex flows over the entire flight envelope and through an aircraft engine, and computing aircraft noise. Some of these flows are dominated by unsteady vortices of disparate scales, often highly turbulent, and they call for higher-order methods. As these tools will be integral components of a multi-disciplinary optimization environment, they must be efficient to impact design. Ultimately, the accuracy, efficiency, robustness, scalability and geometric flexibility will determine which methods will be adopted in the design process. This article explores these aspects and identifies pacing items.
Large eddy simulation for predicting turbulent heat transfer in gas turbines
Authors: Tafti Danesh K. , He Long , Nagendra K.
Published: July 2014

Blade cooling technology will play a critical role in the next generation of propulsion and power generation gas turbines. Accurate prediction of blade metal temperature can avoid the use of excessive compressed bypass air and allow higher turbine inlet temperature, increasing fuel efficiency and decreasing emissions. Large eddy simulation (LES) has been established to predict heat transfer coefficients with good accuracy under various non-canonical flows, but is still limited to relatively simple geometries and low Reynolds numbers. It is envisioned that the projected increase in computational power combined with a drop in price-to-performance ratio will make system-level simulations using LES in complex blade geometries at engine conditions accessible to the design process in the coming one to two decades. In making this possible, two key challenges are addressed in this paper: working with complex intricate blade geometries and simulating high-Reynolds-number (
Re
) flows. It is proposed to use the immersed boundary method (IBM) combined with LES wall functions. A ribbed duct at
Re
=20 000 is simulated using the IBM, and a two-pass ribbed duct is simulated at
Re
=100 000 with and without rotation (rotation number
Ro
=0.2) using LES with wall functions. The results validate that the IBM is a viable alternative to body-conforming grids and that LES with wall functions reproduces experimental results at a much lower computational cost.