bluuebunny/crossref_metadata_2025 huggingface dataset:
Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks
Authors: Marbach Daniel , Roy Sushmita , Ay Ferhat , Meyer Patrick E. , Candeias Rogerio , Kahveci Tamer , Bristow Christopher A. , Kellis Manolis
Published: March 2012

Gaining insights on gene regulation from large-scale functional data sets is a grand challenge in systems biology. In this article, we develop and apply methods for transcriptional regulatory network inference from diverse functional genomics data sets and demonstrate their value for gene function and gene expression prediction. We formulate the network inference problem in a machine-learning framework and use both supervised and unsupervised methods to predict regulatory edges by integrating transcription factor (TF) binding, evolutionarily conserved sequence motifs, gene expression, and chromatin modification data sets as input features. Applying these methods to Drosophila melanogaster, we predict ∼300,000 regulatory edges in a network of ∼600 TFs and 12,000 target genes. We validate our predictions using known regulatory interactions, gene functional annotations, tissue-specific expression, protein–protein interactions, and three-dimensional maps of chromosome conformation. We use the inferred network to identify putative functions for hundreds of previously uncharacterized genes, including many in nervous system development, which are independently confirmed based on their tissue-specific expression patterns. Last, we use the regulatory network to predict target gene expression levels as a function of TF expression, and find significantly higher predictive power for integrative networks than for motif or ChIP-based networks. Our work reveals the complementarity between physical evidence of regulatory interactions (TF binding, motif conservation) and functional evidence (coordinated expression or chromatin patterns) and demonstrates the power of data integration for network inference and studies of gene regulation at the systems level.
The CHD3 Remodeler PICKLE Associates with Genes Enriched for Trimethylation of Histone H3 Lysine 27
Authors: Zhang Heng , Bishop Brett , Ringenberg Whitney , Muir William M. , Ogas Joe
Published: March 2012

In Arabidopsis (Arabidopsis thaliana), the ATP-dependent chromatin remodeler PICKLE (PKL) determines expression of genes associated with developmental identity. PKL promotes the epigenetic mark trimethylation of histone H3 lysine 27 (H3K27me3) that facilitates repression of tissue-specific genes in plants. It has previously been proposed that PKL acts indirectly to promote H3K27me3 by promoting expression of the POLYCOMB REPRESSIVE COMPLEX2 complex that generates H3K27me3. We undertook expression and chromatin immunoprecipitation analyses to further characterize the contribution of PKL to gene expression and developmental identity. Our expression data support a critical and specific role for PKL in expression of H3K27me3-enriched loci but do not support a role for PKL in expression of POLYCOMB REPRESSIVE COMPLEX2. Moreover, our chromatin immunoprecipitation data reveal that PKL protein is present at the promoter region of multiple H3K27me3-enriched loci, indicating that PKL directly acts on these loci. In particular, we find that PKL is present at LEAFY COTYLEDON1 and LEAFY COTYLEDON2 during germination, which is when PKL acts to repress these master regulators of embryonic identity. Surprisingly, we also find that PKL is present at the promoters of actively transcribed genes that are ubiquitously expressed such as ACTIN7 and POLYUBIQUITIN10 that do not exhibit PKL-dependent expression. Taken together, our data contravene the previous model of PKL action and instead support a direct role for PKL in determining levels of H3K27me3 at repressed loci. Our data also raise the possibility that PKL facilitates a common chromatin remodeling process that is not restricted to H3K27me3-enriched regions.
Thioredoxin Redox Regulates ATPase Activity of Magnesium Chelatase CHLI Subunit and Modulates Redox-Mediated Signaling in Tetrapyrrole Biosynthesis and Homeostasis of Reactive Oxygen Species in Pea Plants
Authors: Luo Tao , Fan Tingting , Liu Yinan , Rothbart Maxi , Yu Jing , Zhou Shuaixiang , Grimm Bernhard , Luo Meizhong
Published: March 2012

The chloroplast thioredoxins (TRXs) function as messengers of redox signals from ferredoxin to target enzymes. In this work, we studied the regulatory impact of pea (Pisum sativum) TRX-F on the magnesium (Mg) chelatase CHLI subunit and the enzymatic activation of Mg chelatase in vitro and in vivo. In vitro, reduced TRX-F activated the ATPase activity of pea CHLI and enhanced the activity of Mg chelatase reconstituted from the three recombinant subunits CHLI, CHLD, and CHLH in combination with the regulator protein GENOMES UNCOUPLED4 (GUN4). Yeast two-hybrid and bimolecular fluorescence complementation assays demonstrated that TRX-F physically interacts with CHLI but not with either of the other two subunits or GUN4. In vivo, virus-induced TRX-F gene silencing (VIGS-TRX-F) in pea plants did not result in an altered redox state of CHLI. However, simultaneous silencing of the pea TRX-F and TRX-M genes (VIGS-TRX-F/TRX-M) resulted in partially and fully oxidized CHLI in vivo. VIGS-TRX-F/TRX-M plants demonstrated a significant reduction in Mg chelatase activity and 5-aminolevulinic acid synthesizing capacity as well as reduced pigment content and lower photosynthetic capacity. These results suggest that, in vivo, TRX-M can compensate for a lack of TRX-F and that both TRXs act as important redox regulators of Mg chelatase. Furthermore, the silencing of TRX-F and TRX-M expression also affects gene expression in the tetrapyrrole biosynthesis pathway and leads to the accumulation of reactive oxygen species, which may also serve as an additional signal for the transcriptional regulation of photosynthesis-associated nuclear genes.
A bZIP Protein, VIP1, Is a Regulator of Osmosensory Signaling in Arabidopsis
Authors: Tsugama Daisuke , Liu Shenkui , Takano Tetsuo
Published: March 2012

Abscisic acid is a stress-related phytohormone that has roles in dehydration and rehydration. In Arabidopsis (Arabidopsis thaliana), two genes that inactivate abscisic acid, CYP707A1 and CYP707A3, are rapidly up-regulated upon rehydration. The factors that regulate CYP707A1/3 are not well characterized. We expressed a bZIP protein, VIP1, as a green fluorescent protein fusion protein in Arabidopsis and found that the nuclear localization of VIP1 was enhanced within 10 min after rehydration. A yeast one-hybrid assay revealed that the amino-terminal region of VIP1 has transcriptional activation potential. In a transient reporter assay using Arabidopsis protoplasts, VIP1 enhanced the promoter activities of CYP707A1/3. In gel shift and chromatin immunoprecipitation analyses, VIP1 directly bound to DNA fragments of the CYP707A1/3 promoters. Transgenic plants expressing VIP1-green fluorescent protein were found to overexpress CYP707A1/3 mRNAs. The time course of nuclear-cytoplasmic shuttling of VIP1 was consistent with the time courses of the expression of CYP707A1/3. These results suggest that VIP1 functions as a regulator of osmosensory signaling in Arabidopsis.
Dibromodiphenylstannane: isolated centrosymmetric dimers as a new structure motif for the intermolecular association of diorganotin(IV) dihalides
Authors: Ye Fei , Reuter Hans
Published: March 2012

In the crystalline state, the low-melting title compound [common name: diphenyltin(IV) dibromide], [SnBr2(C6H5)2], consists of distorted tetrahedral molecules with compressed halide and enlarged carbon opening angles of 102.741 (9) and 123.53 (8)°, respectively, and Sn—C and Sn—Br bond lengths of 2.109 (2)/2.113 (2) and 2.4710 (3)/2.4947 (3) Å, respectively. Intermolecular Sn...Br interactions, typical for diorganotin(IV) dihalides,R2SnHal2(with Hal = Cl, Br, I), and sterically less demanding organic groups lead to the formation of a hitherto unknown association pattern consisting of centrosymmetric dimers with an antiparallel orientation of the dipole moments and two weak intermolecular Sn...Br distances of 3.8482 (3) Å between one of the two Br atoms and its neighbouring Sn atom, andvice versa. The second Br atom is not involved in intermolecular interactions and lies somewhat outside the association plane that, therefore, is not coplanar [interplanar angle = 1.750 (2)°] with the tin–halide plane. The new structure motif of intermolecular tin–halide interaction can be classified as 2ai, which indicates the number of molecules (i.e.`2') composing the oligomer, the antiparallel orientation (i.e.`a') of their dipole moments and the centre of symmetry (i.e.`i') giving rise to the association pattern.
Elevational trends in butterfly phenology: implications for species responses to climate change
Authors: ILLÁN JAVIER GUTIÉRREZ , GUTIÉRREZ DAVID , DÍEZ SONIA B. , WILSON ROBERT J.
Published: March 2012

1. Impacts of global change on the distribution, abundance, and phenology of species have been widely documented. In particular, recent climate change has led to widespread changes in animal and plant seasonality, leading to debate about its potential to cause phenological mismatches among interacting taxa.

2. In mountainous regions, populations of many species show pronounced phenological gradients over short geographic distances, presenting the opportunity to test for effects of climate on phenology, independent of variation in confounding factors such as photoperiod.

3. Here we show for 32 butterfly species sampled for five years over a 1700 m gradient (560–2260 m) in a Mediterranean mountain range that, on average, annual flight period is delayed with elevation by 15–22 days per kilometre. Species mainly occurring at low elevations in the region, and to some extent those flying earlier in the year, showed phenological delays of 23–36 days per kilometre, whereas the flight periods of species that occupy high elevations, or fly in late summer, were consistently more synchronised over the elevation gradient.

4. Elevational patterns in phenology appear to reflect a narrowing phenological window of opportunity for larval and adult butterfly activity of high elevation and late‐flying species.

5. Here, we speculate as to the causes of these patterns, and the consequences for our ability to predict species responses to climate change. Our results raise questions about the use of space–time substitutions in predicting phenological responses to climate change, since traits relating to flight period and environmental associations may influence the capacity of species to adapt to changing climates.
The transcription factor Grainy head and the steroid hormone ecdysone cooperate during differentiation of the skin of Drosophila melanogaster
Authors: Gangishetti U. , Veerkamp J. , Bezdan D. , Schwarz H. , Lohmann I. , Moussian B.
Published: March 2012

The arthropod epidermis is an epithelium that deposits the apical cuticle, which is a stratified extracellular matrix (ECM) protecting the animal against pathogens, preventing dehydration and also serving as an exoskeleton. Differentiation of the cuticle conceivably implies coordinated production, secretion and localization of its components. The underlying molecular mechanisms are poorly explored. In this work, we show that the transcription factor Grainy head and the steroid hormone ecdysone drive the production of two partially overlapping sets of cuticle factors. Nevertheless, Grainy head is needed to modulate the expression of ecdysone signalling factors; the significance of this cross‐talk is yet unclear. In addition, we found that ecdysone signalling negatively regulates its own impact. In conclusion, our findings suggest that at least two independently triggered pathways have evolved in parallel to cooperatively ensure the stereotypic implementation of the cuticle. As Grainy head is also essential for epithelial differentiation in vertebrates, we speculate that it acts to decode the ancient skin programme common to all animals. Full differentiation of the skin necessitates a second, complementing taxon‐specific programme that requires its own decoder, which is represented by ecdysone in arthropods, whereas the vertebrate specific one remains to be identified.
Resistance to spiromesifen in Trialeurodes vaporariorum is associated with a single amino acid replacement in its target enzyme acetyl‐coenzyme A carboxylase
Authors: Karatolos N. , Williamson M. S. , Denholm I. , Gorman K. , ffrench‐Constant R. , Nauen R.
Published: March 2012

Spiromesifen is a novel insecticide and is classed as a tetronic acid derivative. It targets the insects' acetyl‐coenzyme A carboxylase (ACCase) enzyme, causing a reduction in lipid biosynthesis. At the time of this publication, there are no reports of resistance to this class of insecticides in insects although resistance has been observed in several mite species. The greenhouse whitefly Trialeurodes vaporariorum (Westwood) is a serious pest of protected vegetable and ornamental crops in temperate regions of the world and spiromesifen is widely used in its control. Mortality rates of UK and European populations of T. vaporariorum to spiromesifen were calculated and up to 26‐fold resistance was found. We therefore sought to examine the molecular mechanism underlying spiromesifen resistance in this important pest. Pre‐treatment with piperonyl butoxide did not synergize spiromesifen, suggesting a target‐site resistance mechanism. The full length ACCase gene was sequenced for a range of T. vaporariorum strains and a strong association was found between spiromesifen resistance and a glutamic acid substitution with lysine in position 645 (E645K) of this gene. A TaqMan allelic discrimination assay confirmed these findings. Although this resistance is not considered sufficient to compromise the field performance of spiromesifen, this association of E645K with resistance is the first report of a potential target site mechanism affecting an ACCase inhibitor in an arthropod species.
Sindbis virus induces the production of a novel class of endogenous siRNAs in Aedes aegypti mosquitoes
Authors: Adelman Z. N. , Anderson M. A. E. , Liu M. , Zhang L. , Myles K. M.
Published: March 2012

Small RNA regulatory pathways are used to control the activity of transposons, regulate gene expression and resist infecting viruses. We examined the biogenesis of mRNA‐derived endogenous short‐interfering RNAs (endo‐siRNAs) in the disease vector mosquito Aedes aegypti. Under standard conditions, mRNA‐derived endo‐siRNAs were produced from the bidirectional transcription of tail−tail overlapping gene pairs. Upon infection with the alphavirus, Sindbis virus (SINV), another class of mRNA‐derived endo‐siRNAs was observed. Genes producing SINV‐induced endo‐siRNAs were not enriched for overlapping partners or nearby genes, but were enriched for transcripts with long 3′ untranslated regions. Endo‐siRNAs from this class derived uniformly from the entire length of the target transcript, and were found to regulate the transcript levels of the genes from which they were derived. Strand‐specific quantitative PCR experiments demonstrated that antisense strands of targeted mRNA genes were produced to exonic, but not intronic regions. Finally, small RNAs mapped to both sense and antisense strands of exon−exon junctions, suggesting double‐stranded RNA precursors to SINV‐induced endo‐siRNAs may be synthesized from mature mRNA templates. These results suggest additional complexity in small RNA pathways and gene regulation in the presence of an infecting virus in disease vector mosquitoes.
Detection and speciation of brominated flame retardants in high‐impact polystyrene (HIPS) polymers
Authors: HOLBROOK R.D. , DAVIS J.M. , SCOTT K.C.K. , SZAKAL C.
Published: March 2012

Polymeric materials have been suggested as possible environmental sources of persistent organic pollutants such as flame retardants. In situ, micrometre‐scale characterization techniques for polymer matrix containing flame retardants may provide some insight into the dominant environmental transfer mechanism(s) of these brominated compounds. In this work, we demonstrate that micro X‐ray fluorescence spectroscopy (μXRF), focused ion beam scanning electron microscopy (FIB‐SEM) combined with energy dispersive X‐ray spectroscopy (EDS), and time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) are promising techniques for the elemental and chemical identification of brominated fire retardant compounds (such as the deca‐congener of polybrominated diphenyl ether, BDE‐209) within polymeric materials (e.g. high‐impact polystyrene or HIPS). Data from μXRF demonstrated that bromine (Br) inclusions were evenly distributed throughout the HIPS samples, whereas FIB SEM‐EDS analysis revealed that small antimony (Sb) and Br inclusions are present, and regionally higher concentrations of Br surround the Sb inclusions (compared to the bulk material). Four prominent mass‐to‐charge ratio peaks (m/z 485, 487, 489 and 491) that correspond to BDE‐209 were identified by ToF‐SIMS and can be used to chemically distinguish this molecule on the surface of polymeric materials with respect to other brominated organic molecules. These techniques can be important in any study that investigates the route of entry to the environmental surroundings of BDE‐containing materials.
Neurosurgery in the age of Cushing: the achievement of Leonard Lindon
Authors: Simpson Donald
Published: March 2012

Leonard Lindon was the first neurosurgeon on the staff of the Royal Adelaide Hospital, and headed this hospital's neurosurgical service from 1931 to 1951, with an interruption from war service. Like other early neurosurgeons, Lindon began as a general surgeon. In 1929, when he was well established in his surgical practice, he took unpaid leave from his hospital duties to undertake a study tour of neurosurgical centres in Europe and North America.

Lindon visited the London Hospital, where Hugh Cairns, like him, an Adelaide medical graduate and veteran of Gallipoli, was establishing a modern neurosurgical service. Lindon also visited Harvey Cushing in Boston, USA. Cushing was then at the zenith of his reputation as the master of a safe neurosurgical operative technique; he was also famous for his contributions in the neurosciences. Lindon was deeply impressed by Cushing's philosophy and his operative methods. When Lindon returned to Adelaide in 1930, he prepared a plan for a neurosurgical unit in Adelaide, and over the next 20 years, he achieved some of his aims. In this plan, Lindon gave priority to the management of head injuries as a role for neurosurgeons.
The Social Communication Intervention Project: a randomized controlled trial of the effectiveness of speech and language therapy for school‐age children who have pragmatic and social communication problems with or without autism spectrum disorder
Authors: Adams Catherine , Lockton Elaine , Freed Jenny , Gaile Jacqueline , Earl Gillian , McBean Kirsty , Nash Marysia , Green Jonathan , Vail Andy , Law James
Published: March 2012

Background: Children who show disproportionate difficulty with the pragmatic as compared with the structural aspects of language are described as having pragmatic language impairment (PLI) or social communication disorder (SCD). Some children who have PLI also show mild social impairments associated with high‐functioning autism or autism spectrum disorder (ASD). There is little robust evidence of effectiveness of speech–language interventions which target the language, pragmatic or social communication needs of these children.

Aims: To evaluate the effectiveness of an intensive manualized social communication intervention (SCIP) for children who have PLI with or without features of ASD.

Methods & Procedures: In a single‐blind RCT design, 88 children with pragmatic and social communication needs aged 5;11–10;8, recruited from UK speech and language therapy services, were randomly assigned in a 2:1 ratio to SCIP or to treatment‐as‐usual. Children in the SCIP condition received up to 20 sessions of direct intervention from a specialist research speech and language therapist working with supervised assistants. All therapy content and methodology was derived from an intervention manual. A primary outcome measure of structural language and secondary outcome measures of narrative, parent‐reported pragmatic functioning and social communication, blind‐rated perceptions of conversational competence and teacher‐reported ratings of classroom learning skills were taken pre‐intervention, immediately post‐intervention and at 6‐month follow‐up. Analysis was by intention to treat.

Outcomes & Results: No significant treatment effect was found for the primary outcome measure of structural language ability or for a measure of narrative ability. Significant treatment effects were found for blind‐rated perceptions of conversational competence, for parent‐reported measures of pragmatic functioning and social communication, and for teacher‐reported ratings of classroom learning skills.

Conclusions & Implications: There is some evidence of an intervention effect on blind and parent/teacher‐reported communication outcomes, but not standardized language assessment outcomes, for 6–11‐year‐old children who have pragmatic and social communication needs. These findings are discussed in the context of the increasingly central role of service user outcomes in providing evidence for an intervention. The substantial overlap between the presence of PLI and ASD (75%) across the whole cohort suggests that the intervention may also be applicable to some verbally able children with ASD who have pragmatic communication needs.
Spatially restricted actin‐regulatory signaling contributes to synapse morphology
Authors: Nicholson Daniel A. , Cahill Michael E. , Tulisiak Christopher T. , Geinisman Yuri , Penzes Peter
Published: March 2012

J. Neurochem. (2012) 121, 852–860.

The actin cytoskeleton in dendritic spines is organized into microdomains, but how signaling molecules that regulate actin are spatially governed is incompletely understood. Here we examine how the localization of the RacGEF kalirin‐7, a well‐characterized regulator of actin in spines, varies as a function of post‐synaptic density area and spine volume. Using serial section electron microscopy, we find that extrasynaptic, but not synaptic, expression of kalirin‐7 varies directly with synapse size and spine volume. Moreover, we find that overall expression levels of kalirin‐7 differ in spines bearing perforated and non‐perforated synapses, due primarily to extrasynaptic pools of kalirin‐7 expression in the former. Overall, our findings indicate that kalirin‐7 is differentially compartmentalized in spines as a function of both synapse morphology and spine size.
Product Replacement Bias in Inflation and Its Consequences for Monetary Policy
Authors: WEBER HENNING
Published: March 2012

The paper examines a New Keynesian model with product entry and exit and with two types of households. Households consume different product baskets, and therefore, face different inflation rates. The statistical bureau used in the model measures aggregate inflation, but observes product entry with a probabilistic delay. Consequently, measured inflation suffers from product replacement bias with respect to aggregate inflation. Measured inflation is less volatile but more persistent than aggregate inflation, and the correlation between aggregate inflation and aggregate output is lower than the correlation between measured inflation and measured output. When monetary policy responds to measured variables, it stabilizes aggregate inflation insufficiently. Nevertheless, under discretionary monetary policy, responding to measured variables improves welfare.
Real Exchange Rates and Productivity: Evidence from Asia
Authors: KAKKAR VIKAS , YAN ISABEL
Published: March 2012

This paper examines a productivity‐based explanation of the long‐run real exchange rate movements of six Asian economies. Using industry level data, we construct total factor productivities (TFPs) for the tradable and nontradable sectors. We find that (i) within each country the relative price of nontradable goods is cointegrated with the sectoral TFP differential, and (ii) the real exchange rates are cointegrated with the home and foreign sectoral TFP differentials. Using the predicted real exchange rate as a measure of the “long‐run equilibrium,” we find that most Asian economies’ real exchange rates were overvalued before the Asian Financial Crisis.
Uncertainty Over Models and Data: The Rise and Fall of American Inflation
Authors: PRUITT SETH
Published: March 2012

Economic agents who are uncertain of their economic model learn, and this learning is sensitive to the presence of data uncertainty. I investigate this idea in a framework that successfully describes inflation as a learning Federal Reserve’s optimal policy but fails to satisfactorily motivate these policy shifts. I modify the framework to account for data uncertainty: the learning process is made more sluggish by its presence. Consequently, the estimated model provides an explanation for the rise and fall in inflation: the concurrent rise and fall in the perceived Philips curve trade‐off between inflation and unemployment.
One for Some or One for All? Taylor Rules and Interregional Heterogeneity
Authors: COIBION OLIVIER , GOLDSTEIN DANIEL
Published: March 2012

We document a novel empirical phenomenon: the U.S. Federal Reserve appears to set interest rates partly in response to regional economic disparities. This result is robust even after controlling for factors such as the central bank's forecasts and a battery of explanatory variables. We argue that this likely does not reflect an explicit concern about regional differences by policymakers but instead can be explained by a model with nonlinear regional Phillips curves. Consistent with the predictions of this model, we find that the Federal Reserve responds disproportionately to fluctuations in low unemployment states. Alternative explanations cannot account for this finding.
Sacrifice Ratio in a Medium‐Scale New Keynesian Model
Authors: ASCARI GUIDO , ROPELE TIZIANO
Published: March 2012

A medium‐scale macroeconomic model, with a number of nominal and real frictions that have been shown to be important for explaining observed aggregate fluctuations, is capable to quantitatively account for the empirically estimated sacrifice ratio after a disinflationary monetary policy. This finding, however, is sensitive to the degrees of price and wage indexation to past inflation and, to a less extent, to the price and wage Calvo probabilities.
Hedge Funds and Chapter 11
Authors: JIANG WEI , LI KAI , WANG WEI
Published: March 2012

This paper studies the presence of hedge funds in the Chapter 11 process and their effects on bankruptcy outcomes. Hedge funds strategically choose positions in the capital structure where their actions could have a bigger impact on value. Their presence, especially as unsecured creditors, helps balance power between the debtor and secured creditors. Their effect on the debtor manifests in higher probabilities of the latter's loss of exclusive rights to file reorganization plans, CEO turnover, and adoptions of key employee retention plan, while their effect on secured creditors manifests in higher probabilities of emergence and payoffs to junior claims.
Selective Publicity and Stock Prices
Authors: SOLOMON DAVID H.
Published: March 2012

I examine how media coverage of good and bad corporate news affects stock prices, by studying the effect of investor relations (IR) firms. I find that IR firms “spin” their clients' news, generating more media coverage of positive press releases than negative press releases. This spin increases announcement returns. Around earnings announcements, however, IR firms cannot spin the news and their clients' returns are significantly lower. This pattern is consistent with positive media coverage increasing investor expectations, creating disappointment around hard information. Using reporter connections and geographical links, I argue that IR firms causally affect both media coverage and returns.
Individual Investor Trading and Return Patterns around Earnings Announcements
Authors: KANIEL RON , LIU SHUMING , SAAR GIDEON , TITMAN SHERIDAN
Published: March 2012

This paper provides evidence of informed trading by individual investors around earnings announcements using a unique data set of NYSE stocks. We show that intense aggregate individual investor buying (selling) predicts large positive (negative) abnormal returns on and after earnings announcement dates. We decompose abnormal returns following the event into information and liquidity provision components, and show that about half of the returns can be attributed to private information. We also find that individuals trade in both return‐contrarian and news‐contrarian manners after earnings announcements. The latter behavior has the potential to slow the adjustment of prices to earnings news.
A Simple Way to Estimate Bid‐Ask Spreads from Daily High and Low Prices
Authors: CORWIN SHANE A. , SCHULTZ PAUL
Published: March 2012

We develop a bid‐ask spread estimator from daily high and low prices. Daily high (low) prices are almost always buy (sell) trades. Hence, the high–low ratio reflects both the stock's variance and its bid‐ask spread. Although the variance component of the high–low ratio is proportional to the return interval, the spread component is not. This allows us to derive a spread estimator as a function of high–low ratios over 1‐day and 2‐day intervals. The estimator is easy to calculate, can be applied in a variety of research areas, and generally outperforms other low‐frequency estimators.
Automated Texture Recognition of Quartz Sand Grains for Forensic Applications*
Authors: Newell Andrew J. , Morgan Ruth M. , Griffin Lewis D. , Bull Peter A. , Marshall John R. , Graham Giles
Published: March 2012

Abstract:  Quartz sand surface texture analysis has been automated for the first time for forensic application. The derived Basic Image Features (BIFs) provide computer‐generated texture recognition from preexisting data sets. The technique was applied to two distinct classification problems; first, the ability of the system to discriminate between (quartz) sand grains with upturned plate features (indicative of eolian, global sand sea environments) and grains that do not exhibit these features. A success rate of grain classification of 98.8% was achieved. Second, to test the ability of the computer recognition system to identify specific energy levels of formation of the upturned plate surface texture features. Such recognition ability has to date been beyond manual geological interpretation. The discrimination performance was enhanced to an exact classification success rate of 81%. The enhanced potential for routine forensic investigation of the provenance of common quartz sand is indicated.
Bayesian Networks and the Value of the Evidence for the Forensic Two‐Trace Transfer Problem*
Authors: Gittelson Simone , Biedermann Alex , Bozza Silvia , Taroni Franco
Published: March 2012

Abstract: Forensic scientists face increasingly complex inference problems for evaluating likelihood ratios (LRs) for an appropriate pair of propositions. Up to now, scientists and statisticians have derived LR formulae using an algebraic approach. However, this approach reaches its limits when addressing cases with an increasing number of variables and dependence relationships between these variables. In this study, we suggest using a graphical approach, based on the construction of Bayesian networks (BNs). We first construct a BN that captures the problem, and then deduce the expression for calculating the LR from this model to compare it with existing LR formulae. We illustrate this idea by applying it to the evaluation of an activity level LR in the context of the two‐trace transfer problem. Our approach allows us to relax assumptions made in previous LR developments, produce a new LR formula for the two‐trace transfer problem and generalize this scenario tontraces.
Effect of a chlorhexidine mouthrinse on plaque, gingival inflammation and staining in gingivitis patients: a systematic review
Authors: Van Strydonck Daniëlle A. C. , Slot Dagmar E. , Van der Velden Ubele , Van der Weijden Fridus
Published: March 2012

Aim

To systematically evaluate the efficacy of chlorhexidine (CHX) mouthrinses on plaque, gingival inflammation and staining in gingivitis patients.

Material & Methods

Medline, EMBASE and Cochrane Central Register of Controlled Trials were searched through April 2011. Randomized controlled clinical trials comparing CHX to placebo/control mouthrinses or oral hygiene (OH) ≥4 weeks were included.

Results

Among 1355 titles, 30 publications fulfilled the selection criteria. Meta‐analysis (MA) showed significant weighted mean differences (WMD) favouring CHX. This was −0.39 [95% CI: −0.70; −0.08] for the Plaque Index Silness & Löe, −0.67 [95% CI: −0.82; −0.52] for the Plaque‐Index Quigley & Hein (PIQH), −0.32 [95% CI: −0.42; −0.23] for the Gingival Index (GI), −0.08 [95% CI: −0.10; −0.05] for the bleeding aspect of the GI, −0.21 [95% CI: −0.37; −0.04] for the Papillary BIeeding Index, −0.16 [95% CI: −0.26; −0.07] for Bleeding on Marginal Probing and 0.91 [95% CI: 0.12;1.70] for the Lobene Stain Index. MA of studies with a low risk of author‐estimated bias showed a WMD of −0.68 [95% CI: −0.85; −0.51] for the PIQH and −0.24 [95% CI: −0.29; −0.20] for the GI in favour of CHX. Relative to control, the reduction with CHX for plaque was 33% and for gingivitis 26%. CHX rinsing groups demonstrated significantly more staining.

Conclusions

In gingivitis patients, CHX mouthrinses together with OH versus placebo‐ or control mouthrinse provide significant reductions in plaque and gingivitis scores, but a significant increase in staining score.
Fifty years of natural succession in Swiss forest reserves: changes in stand structure and mortality rates of oak and beech
Authors: Rohner Brigitte , Bigler Christof , Wunder Jan , Brang Peter , Bugmann Harald
Published: March 2012

Question

What are the drivers of structural changes and mortality in oak–beech forests over 50 yrs of natural succession?

Location

Twelve unmanaged forest sites, comprising a large environmental gradient in theSwiss lowlands.

Method

By using repeated inventory data from more than 17 600 individually tagged trees, the dynamics of oak–beech stands over the past 50 yrs were analysed. Generalized linear mixed‐effects models were fitted to quantify annual mortality rates of oak and beech based onDBH, stand basal area, precipitation and slope.

Results

Stand basal area increased, whereas tree density decreased over time. At most sites, the relative importance of oak decreased gradually compared to beech. Mortality increased over time for both oak and beech, but the increase was stronger for oak. Oak and beech mortality decreased with increasingDBHand tended to increase with precipitation. Additionally, oak mortality increased with stand basal area, whereas no such trend was found for beech.

Conclusion

Our study indicates that mortality inCentralEuropean oak–beech forests is driven by a combination of stand structures (i.e. tree size and stand basal area) and climate. However, the influence of climate on oak mortality is comparably low. Increasing oak mortality with stand basal area is a plausible consequence of its lower relative competitiveness and higher demand for light. Thus, in forests developing towards higher stand basal area, the ecologically important oak is increasingly outcompeted by beech, unless competition is reduced through management or disturbances.
Late Dialysis Start Did Not Affect Long‐Term Outcome in Japanese Dialysis Patients: Long‐Term Prognosis From Japanese Society of Dialysis Therapy Registry
Authors: Yamagata Kunihiro , Nakai Shigeru , Iseki Kunitoshi , Tsubakihara Yoshiharu ,   The Committee of Renal Data Registry of the Japanese Society for Dialysis Therapy
Published: March 2012

Early initiation of dialysis had been considered one of the most important methods for better prognosis of dialysis patients. One of the reasons for this was that long‐term as well as short‐term prognosis was poor with late initiation of dialysis. In this study, we analyzed the effects of residual renal function and comorbidity on both short‐ and long‐term outcomes of ESRD patients. The subjects of this study were 20 854 patients who started renal replacement therapy (RRT) in 1989 and 1990, when we conducted national surveillance for new ESRD patients. The effects of glomerular filtration rate (GFR) at dialysis start and comorbidity conditions on survival were measured. Mortality hazard ratio (HR) was calculated using a Cox proportional hazard model. Multivariate analysis included pre‐dialysis estimated GFR, age, sex, and underlying renal disease. The mean age of the subjects was 57.7 years old. Mean GFR at dialysis initiation was 5.00 mL/min per 1.73 m2 and GFR was significantly higher in patients with diabetes. The median survival time from the start of dialysis was 69 months, excluding subjects who died within 3 months; 1‐year survival was 89.7%, while 2‐year, 3‐year, 5‐year, 10‐year, and 15‐year cumulative survival rates were 79.3%, 71.1%, 57.8%, 37.3%, and 26.1%, respectively. For mortality risks, the higher the GFR at dialysis initiation, the worse the HR for mortality in both short‐term and long‐term prognoses by unadjusted analysis. However, after adjustments for age, gender, underlying renal diagnosis, and symptom at dialysis initiation, both late and early initiation of RRT did not affect long‐term prognosis.
Addressing the Extreme Assumptions of Presumed Linkings
Authors: Dorans Neil J. , Middleton Kyndra
Published: March 2012

The interpretability of score comparisons depends on the design and execution of a sound data collection plan and the establishment of linkings between these scores. When comparisons are made between scores from two or more assessments that are built to different specifications and are administered to different populations under different conditions, the validity of the comparisons hinges on untestable assumptions. For example, tests administered across different disability groups or tests administered to different language groups produce scores for which implicit linkings are presumed to hold. Presumed linking makes use of extreme assumptions to produce links between scores on tests in the absence of common test material or equivalent groups of test takers. These presumed linkings lead to dubious interpretations. This article suggests an approach that indirectly assesses the validity of these presumed linkings among scores on assessments that contain neither equivalent groups nor common anchor material.
The Impact of Model Misspecification on Parameter Estimation and Item‐Fit Assessment in Log‐Linear Diagnostic Classification Models
Authors: Kunina‐Habenicht Olga , Rupp André A. , Wilhelm Oliver
Published: March 2012

Using a complex simulation study we investigated parameter recovery, classification accuracy, and performance of two item‐fit statistics for correct and misspecified diagnostic classification models within a log‐linear modeling framework. The basic manipulated test design factors included the number of respondents (1,000 vs. 10,000), attributes (3 vs. 5), and items (25 vs. 50) as well as different attribute correlations (.50 vs. .80) and marginal attribute difficulties (equal vs. different). We investigated misspecifications of interaction effect parameters under correct Q‐matrix specification and two types of Q‐matrix misspecification. While the misspecification of interaction effects had little impact on classification accuracy, invalid Q‐matrix specifications led to notably decreased classification accuracy. Two proposed item‐fit indexes were more strongly sensitive to overspecification of Q‐matrix entries for items than to underspecification. Information‐based fit indexes AIC and BIC were sensitive to both over‐ and underspecification.
Must We Ration Health Care for the Elderly?
Authors: Callahan Daniel
Published: March 2012

For well over 20 years I have been arguing that someday we will have to ration health care for the elderly. I got started in the mid-1980s when I served on an Office of Technology Assessment panel to assess the likely impact on elderly health care costs of emergent, increasingly expensive medical technologies. They would, the panel concluded, raise some serious problems for the future of Medicare. The panel did not take up what might be done about those costs, but I decided to think about that question and wrote a book called, Setting Limits: Medical Goals in an Aging Society.
Social Justice, Health Disparities, and Culture in the Care of the Elderly
Authors: Dilworth-Anderson Peggye , Pierre Geraldine , Hilliard Tandrea S.
Published: March 2012

This paper addresses two interconnected concepts — health disparities and social justice — as they pertain to screening, diagnosis of disease, and health care access among minority elders in the American society. Health disparities are defined as differences in treatment provided to members of different racial or ethnic groups that are not justified by the underlying health conditions or treatment preferences of patients. Disparities currently exist in many aspects of American health care. For example, when compared to whites, the infant mortality rate is higher for African Americans; health insurance coverage is lower for Latinos and African Americans; and ethnic minorities experience poorer care and survival rates for HIV, even after controlling for other confounding factors including income, insurance, health status, and severity of disease. Among older Americans, health status varies by race, income, and gender. Older minority Americans have consistently been shown to have worse health than whites of the same age group across measures of disease, disability, and self-assessed health. When compared to whites, elderly Latinos have higher rates of diabetes and disabilities, and older African Americans have more chronic conditions.
Effects of disturbance on small mammal community structure in the New Jersey Pinelands, USA
Authors: SHENKO Alicia N. , BIEN Walter F. , SPOTILA James R. , AVERY Harold W.
Published: March 2012

We compared small mammal community composition among undisturbed habitats and habitats disturbed by military operations on Warren Grove Gunnery Range (WGR) in the New Jersey Pinelands. WGR is one of the largest tracts of protected land within this globally rare ecosystem. Disturbance in the form of fire, mowing, soil disruption and logging has had a large effect on small mammal occurrence and distribution. Of the 14 small mammal species that occur in the Pinelands, 9 live on WGR, including large populations of the southern bog lemming (Synaptomys cooperi Baird, 1858) and meadow jumping mouse [Zapus hudsonius (Zimmermann, 1780)]. Simpson's Index of Diversity was 0 for most disturbed sites and was generally greater in wetlands than in uplands. White‐footed mouse [Peromyscus leucopus (Rafinesque, 1818)] was the most common species on WGR and had a dominant effect on species diversity and community similarity indices. It dominated upland habitats and was the only species to occur in several disturbed habitats, whereas all 9 species occurred in wetlands. Principal components analysis indicated that most variation in species diversity was explained by disturbance and differences between upland and wetland habitats, due to presence of white‐footed mice in disturbed and upland sites. Meadow jumping mice, southern bog lemmings and red‐back voles [Myodes gapperi (Vigors, 1830)] were positively correlated with wetland habitats, and pine voles [Microtus pinetorum (Le Conte, 1830)], short‐tail shrews [Blarina brevicauda (Say, 1823)] and eastern chipmunks [Tamias striatus (Linnaeus, 1758)] were associated with uplands. Habitat heterogeneity at WGR, including extensive undisturbed wetlands and uplands supported a rich diversity of small mammal species.
Sea urchin coelomocyte arylsulfatase: a modulator of the echinoderm clotting pathway
Authors: D'ANDREA‐WINSLOW Lisanne , RADKE David W. , UTECHT Tim , KANEKO Takuya , AKASAKA Koji
Published: March 2012

Sea urchin petalloid coelomocytes effectuate the clotting pathway by undergoing a rapid and dynamic cellular transformation that leads to cellular adhesion and wounds closure. We have identified high levels of activity of arylsulfatase (Ars) associated with coelomocytes of the sea urchin Lytechinus variegatus (Lamarck, 1816). Ars activity was extracted from clotted coelomocytes with EDTA and showed high levels of activity up to a 1:100 dilution. Clot formation from isolated coelomic fluid was significantly inhibited by the ARS inhibitor, p‐nitrophenyl phosphate. Ars activity was collected by 80% ethanol precipitation, a diagnostic test previously used in Ars isolation. Cellular extraction studies in the presence and absence of the non‐ionic detergent Triton X‐100 indicated that some Ars activity was present intracellularly, possibly in intracellular membrane‐bound compartments, however the majority of Ars activity was extracted from the extracellular coelomocyte membrane. Polyclonal anti‐sea urchin embryo Ars antibodies recognized a single protein band with an approximate molecular weight of 75 kDa on western blots. Immunofluorescence using the anti‐sea urchin Ars antibody revealed an intracellular and extracellular staining of Ars in both petalloid and filopodial coelomocytes. Taken together, these data indicate that coelomocyte Ars might be involved in cell‐to‐cell crosslinking of surface sulfated polysaccharides vital for clot formation.
Multiannual patterns of influenza A transmission in Chinese live bird market systems
Authors: Pepin Kim M. , Wang Jia , Webb Colleen T. , Smith Gavin J. D. , Poss Mary , Hudson Peter J. , Hong Wenshan , Zhu Huachen , Riley Steven , Guan Yi
Published: March 2012

Please cite this paper as: Pepin et al. (2012) Multiannual patterns of influenza A transmission in Chinese live bird market systems. Influenza and Other Respiratory Viruses DOI: 10.1111/j.1750‐2659.2012.00354.x.

Background  Avian influenza viruses (AIV) cause huge economic losses in poultry industries and pose a substantial threat to human health. However, predicting AIV epizootics and emergence in humans is confounded by insufficient empirical data on the ecology and dynamics of AIV in poultry systems. To address this gap, we quantified incidence patterns for 13 hemagglutinin subtypes of AIV using 6 years of surveillance data that were collected from ten different species of poultry and three different types of poultry holdings (contexts) – retail, wholesale, or farms.

Methods  We collected 42 646 samples in Shantou, China between 2000 and 2006. We screened samples for hemagglutinin subtypes 1–13 of AIV and Avian Paramyxovirus‐type‐1 (APMV‐1) using monospecific antisera in hemagglutination inhibition tests. We analyzed the data to determine seasonality patterns, subtype–host, and subtype–subtype interactions as well as subtype bias in incidence in different contexts.

Results  H3, H6, H9, and APMV‐1 were the most prevalent. No significant seasonality was found when all subtypes were considered together. For most AIV subtypes and APMV‐1, there was subtype specificity for host, context, and coinfection partner. H5 showed the most generalized host usage pattern, followed by H9 and H6.

Conclusion  Subtype‐specific patterns because of host, context, and other subtypes suggest that risk assessments that exclude these details are likely inaccurate. Surveillance should include longitudinal sampling of multiple host species in multiple contexts. Quantitative models of control strategies must consider multiple subtypes, hosts, and source contexts to assess the effectiveness of interventions.