bluuebunny/crossref_metadata_2025 huggingface dataset:
Big Correlations in Little Studies: Inflated fMRI Correlations Reflect Low Statistical Power—Commentary on Vul et al. (2009)
Authors: Yarkoni Tal
Published: May 2009

Vul, Harris, Winkielman, and Pashler (2009) , (this issue) argue that correlations in many cognitive neuroscience studies are grossly inflated due to a widespread tendency to use nonindependent analyses. In this article, I argue that Vul et al.'s primary conclusion is correct, but for different reasons than they suggest. I demonstrate that the primary cause of grossly inflated correlations in whole-brain fMRI analyses is not nonindependence, but the pernicious combination of small sample sizes and stringent alpha-correction levels. Far from defusing Vul et al.'s conclusions, the simulations presented suggest that the level of inflation may be even worse than Vul et al.'s empirical analysis would suggest.
Correlations in Social Neuroscience Aren't Voodoo: Commentary on Vul et al. (2009)
Authors: Lieberman Matthew D. , Berkman Elliot T. , Wager Tor D.
Published: May 2009

Vul, Harris, Winkielman, and Pashler (2009) , (this issue) claim that many brain—personality correlations in fMRI studies are “likely … spurious” (p. 274), and “should not be believed” (p. 285). Several of their conclusions are incorrect. First, they incorrectly claim that whole-brain regressions use an invalid and “nonindependent” two-step inferential procedure, a determination based on a survey sent to researchers that only included nondiagnostic questions about the descriptive process of plotting one's data. We explain how whole-brain regressions are a valid single-step method of identifying brain regions that have reliable correlations with individual difference measures. Second, they claim that large correlations from whole-brain regression analyses may be the result of noise alone. We provide a simulation to demonstrate that typical fMRI sample sizes will only rarely produce large correlations in the absence of any true effect. Third, they claim that the reported correlations are inflated to the point of being “implausibly high.” Though biased post hoc correlation estimates are a well-known consequence of conducting multiple tests, Vul et al. make inaccurate assumptions when estimating the theoretical ceiling of such correlations. Moreover, their own “meta-analysis suggests that the magnitude of the bias is approximately .12—a rather modest bias.
Correlations and Multiple Comparisons in Functional Imaging: A Statistical Perspective (Commentary on Vul et al., 2009)
Authors: Lindquist Martin A. , Gelman Andrew
Published: May 2009

Vul, Harris, Winkielman, and Pashler (2009), this issue) claim in their article that the correlations reported in fMRI studies are commonly overstated because researchers tend to report only the highest correlations or only those correlations that exceed some threshold. Their article has in a short time given rise to a spirited debate about key statistical issues at the heart of most functional neuroimaging studies. The debate provides a useful opportunity to discuss core statistical issues in neuroimaging and ultimately provides a chance for the field to grow and move forward. This commentary approaches the debate from a fundamentally statistical perspective. We begin by summarizing several of the key points under discussion, followed by our own commentary on these issues from a statistical point of view. We conclude our discussion by contemplating whether it may be time to move beyond the correlation and multiple comparisons framework that is causing so much confusion and instead represent all relevant research questions as parameters in one coherent multilevel model.
Does disturbance of self underlie social cognition deficits in schizophrenia and other psychotic disorders?
Authors: Nelson Barnaby , Sass Louis A. , Thompson Andrew , Yung Alison R. , Francey Shona M. , Amminger G. Paul , McGorry Patrick D.
Published: May 2009

Aim: Although the different approaches to psychosis research have made significant advances in their own fields, integration between the approaches is often lacking. This paper attempts to integrate a strand of cognitive research in psychotic disorders (specifically, social cognition research) with phenomenological accounts of schizophrenia and other psychotic disorders.

Method: The paper is a critical investigation of phenomenological models of disturbed selfhood in schizophrenia in relation to cognitive theories of social cognition in psychotic disorders.

Results: We argue that disturbance of the basic sense of self, as articulated in the phenomenological literature, may underlie the social cognition difficulties present in psychotic disorders. This argument is based on phenomenological thinking about self‐presence (‘ipseity’) being the primary or most basic ground for the intentionality of consciousness – that is, the directedness of consciousness towards others and the world. A disruption in this basic ground of conscious life has a reverberating effect through other areas of cognitive and social functioning. We propose three routes whereby self‐disturbance may compromise social cognition, including dissimilarity, disruption of lived body and disturbed mental coherence.

Conclusions: If this model is supported, then social cognition difficulties may be thought of as a secondary index or marker of the more primary disturbance of self in psychotic disorders. Further empirical work examining the relationship between cognitive and phenomenological variables may be of value in identifying risk markers for psychosis onset, thus contributing to early intervention efforts, as well as in clarifying the essential psychopathological features of schizophrenia and other psychotic disorders.
Untreated psychotic illness in the survivors of violent suicide attempts
Authors: Nielssen Olav B. , Large Matthew M.
Published: May 2009

Background: Recent studies suggest that violence is more common in the first episode of psychosis than after treatment.

Aim: To estimate the proportion of survivors of violent suicide attempts during psychotic illness who had not previously received treatment with antipsychotic medication.

Methods: An audit of the medical records of patients admitted to an inner city trauma centre after having survived a jump of more than 3 m or a self‐inflicted gunshot wound or stab wound to a vital body part.

Results: There were 88 survivors of violent suicide attempts. Thirty‐seven of those had a psychotic illness, including 33 with a schizophrenia‐spectrum psychosis. Of the 37, 18 (48.6%, 95% confidence interval (CI) 32.3–65.0%) had never received treatment for psychosis.

Conclusion: As first episode psychosis is less common than previously treated psychosis, there appears to be a higher risk of violent suicide attempts during the first episode of psychosis than later in the illness.
The Effect of Functional Dentition on Healthy Eating Index Scores and Nutrient Intakes in a Nationally Representative Sample of Older Adults
Authors: Ervin R. Bethene , Dye Bruce A.
Published: May 2009

Objective: The objectives of this study were to examine the associations between functional dentition and the Healthy Eating Index (HEI) scores and nutrient intakes among older adults in the United States. Methods: The sample consisted of 2,560 adults, 60 years and over from the National Health and Nutrition Examination Survey 1999‐2002. We used multivariate linear regression to examine associations between functional dentition and HEI scores or nutrient intakes controlling for the potential confounding effects of age, race/ethnicity, education, smoking status, body mass index (BMI), self‐reported health, and caloric intake. Dentate status was classified as: edentulous (no natural permanent teeth or implants), 1‐20 teeth, or≥21 teeth. A functional dentition was defined as having 21 or more teeth present. HEI scores and nutrient intakes were based on one 24‐hour dietary recall. Results: Males with a functional dentition consumed slightly more fruit and had higher alpha‐ and beta‐carotene intakes than edentulous males. Females with any natural teeth had higher vitamin C intakes than edentulous females. There were no significant associations between dentate status and any of the remaining HEI scores or nutrient intakes for either sex. Conclusions: Having a functional dentition did not contribute substantially to higher HEI scores or nutrient intakes in this nationally representative sample of older adults. However, older men and women with no teeth or those who wear dentures consumed fewer servings of fruits and vegetables, especially those rich in carotenes and vitamin C, than those with teeth.
A Health Education Program for Brazilian Public Schoolchildren: The Effects on Dental Health Practice and Oral Health Awareness
Authors: De Farias Irlane Alves , De Araújo Souza Georgia Costa , Ferreira Maria Ângela Fernandes
Published: May 2009

Objectives: Determine the impact of an oral health education program on oral hygiene and the awareness level of elementary schoolchildren. Methods: A total sample of 247 schoolchildren between the ages of 7 and 15 years from the public school system of Parnamirim, Brazil, were selected and randomly allocated to a control (n = 115) and experimental (n = 132) group. Sociodemographic data were recorded and a clinical examination was given to establish the decayed, missing and filled surfaces index (DMFS) and the dmfs index. The visible plaque index (VPI) and gingival bleeding index (GBI) were collected before and after the intervention. A closed‐question questionnaire was applied to the schoolchildren before and after intervention to determine their knowledge of oral health. The experimental group took part in oral health education activities over a 4‐month period. Results: The VPI (P = 0.014; CI 0.24‐0.86) and GBI (P = 0.013; CI 0.28‐0.87) of the experimental group were significantly lower after educational activities. Similarly, the experimental group also obtained a higher number of correct answers on the questionnaire (P < 0.0001; CI 3.73‐26.81). However, there was no association between oral hygiene indicators, VPI (P = 0.311; CI 0.23‐1.60), and GBI (P = 0.927; CI 0.43‐2.16), and the information level of the schoolchildren. Conclusions: Contextualized educational activities in the school routine had positive effects on oral hygiene and the level of information about oral health, although the more informed individuals did not always practice better oral hygiene.
Normalization and binning of historical and multi‐source microsatellite data: overcoming the problems of allele size shift with allelogram
Authors: MORIN PHILLIP A. , MANASTER CARL , MESNICK SARAH L. , HOLLAND ROBERT
Published: May 2009

Microsatellite allele data have long been plagued by size shifts that can at best make it difficult to accurately assign genotypes to allele products, and at worse can cause whole batches of data from different instruments, dates or laboratories to be incorrectly assigned. Although modern genotyping technology (capillary electrophoresis) has overcome many of these problems, concern remains regarding the consistency of scores within a laboratory over time and between laboratories when combining data from multiple sources into a single analysis. There remain a large number of laboratories using older technologies or combining data from multiple sources. In addition, thousands of data sets that could potentially be expanded as samples become available are generally regarded as unusable because of the effort that would be required to validate congruence of genotypes from old and new data sets. We present methods to normalize and bin alleles from multiple data sources using a relatively small set of controls and the freely available program allelogram.
PACT: A Collaborative Team Model for Treating High Conflict Families in Family Court
Authors: Brown Joe H. , Bledsoe Linda , Yankeelov Pamela , Christensen Dana , Rowan Noell L. , Cambron Mary Lou
Published: May 2009

This article describes a court‐community model program for high conflict divorced families that is designed to reduce the level of inter‐parental conflict including: a) child exposure to inter‐parental conflict; and b) the frequency of re‐litigation over residential arrangements and parenting plans. The six‐session (16‐hour) program combines conflict resolution and group/community support. The program provides a “Personal Support Team” and “Personal Plan of Action” to help each parent control emotions and maintain agreement. The results of research conducted to explore the effect of the program on level of triangulation and inter‐parental conflict, as well as the frequency of re‐litigation over parenting plans, residential arrangements, and parenting time are reported.
Families of Origin, Foster Care Experience, and the Transition to Adulthood
Authors: Holland Donna Dea
Published: May 2009

The rising number of young adults transitioning to adulthood from the foster care system has been a focus of prior research. The current study explored foster care youths transitions to adulthood to identify factors that contribute to or inhibit prosocial adult outcomes. Structured data derived from interviews with foster care‐experienced adults and child welfare professionals as well as focus groups with foster care‐experienced adults and foster parents were analyzed using content analysis to examine the transition to adulthood from foster care. Positive or negative life outcomes resulted from two key mechanisms: a) issues related to family of origin (inadequate parenting, abuse); and b) foster care experiences (including a pattern of “drift”). We explore disidentification, a new social psychological concept. Throughout, key players provide policy recommendations for the child welfare system.
Matches in Beliefs Between Teachers and Students, and Success in L2 Attainment: The Georgian Example
Authors: Polat Nihat
Published: May 2009

Abstract: This study addresses matches in beliefs between Georgian English learners and teachers and relationships among beliefs and overall language and grammar achievement, exploring the underlying reasons behind beliefs. Utilizing a mixed‐method design, the researcher collected data through student/teacher questionnaires, evaluation inventories, observations, interviews, and course‐book analyses. Participants included 30 teachers and 40 students. Findings suggested that the overwhelming majority of participants endorsed grammar's significance, considering knowledge of L1 grammar and learning of L2 grammar prerequisites to language learning. Contradicting suggested program course‐books and goals, most teachers/students championed traditional ways of teaching/learning grammar. In addition, unlike the nonmatching group, students in the matching group had higher grammar grades than their overall grades. Testing and observation data indicated that neither matches nor mismatches in beliefs seemed to contribute to overall language achievement.
Initial phase and free-particle wave packet evolution
Authors: Beach Theodore L.
Published: May 2009

The evolution of the free-particle wave function in one dimension is the same as scalar Fresnel diffraction from a one-dimensional structure. Quantum mechanics courses often explore the propagation of Gaussian wave packets, but the diffractionlike mathematics is sufficiently tractable to investigate the propagation of other wave packets, both numerically and analytically. More importantly, the diffraction analogy facilitates the development of an intuitive understanding of the role that the initial phase plays in free-particle wave packet evolution. This article considers some of the effects of the initial phase function on the subsequent evolution of free-particle wave packets in the position representation. These considerations reinforce the idea that the classical mechanics limit embodied in the correspondence principle and formalized in the Ehrenfest theorem is necessarily an incomplete representation of quantum behavior.
Lord Kelvin’s gyrostat and its analogs in physics, including the Lorenz model
Authors: Tong Christopher
Published: May 2009

A gyrostat is a system of bodies whose relative motion does not alter the intrinsic mass distribution of the system. A solid gyrostat is an arbitrary rigid body attached to one or more axisymmetric rotors with their axes fixed in the carrier. A liquid gyrostat is a cavity in a rotating rigid body filled with an inviscid, homogeneous fluid. For certain conditions, gyrostats obey the Volterra equations of motion, a generalization of the Euler equations for a rigid body rotating about a fixed point. The Lorenz model is equivalent to a special case of a gyrostat in a forced, dissipative regime, as is its laboratory analog, the Malkus water wheel. Over a century ago, Lord Kelvin, the gyrostat’s inventor, attempted to formulate mechanical models of the elasticity of matter and the ether, using lattices of linked gyrostats. Opportunities for using gyrostats in the teaching of undergraduate mechanics, nonlinear dynamics, and fluid dynamics are discussed.
The first frontier: High altitude ballooning as a platform for student research experiences in science and engineering
Authors: Larson Shane L. , Armstrong John C. , Hiscock William A.
Published: May 2009

High altitude balloon platforms are ideal for providing hands-on research experiences for students in physics, atmospheric science, engineering, and other aerospace-related disciplines. We describe a basic high altitude balloon platform that can be constructed and operated by undergraduate students. The existing HARBOR and BOREALIS programs are used to illustrate some possible science and engineering research projects that students can pursue as part of a high-altitude flight program.
Ohm’s law for a wire in contact with a thermal reservoir
Authors: Madsen M. J.
Published: May 2009

Ohm’s law is one of the key empirical relations taught in introductory courses on electricity. Students often do a straightforward experiment to measure the current through a resistor as a function of voltage. These experiments typically yield a linear relation between the current and the voltage using carbon film resistors. However, the same measurements on long lengths of conducting wire (such as common wire resistivity kits) typically have a clear nonlinear component. The nonlinear behavior can be modeled using simple principles of heat transfer with a thermal reservoir. Experimental results are shown to agree well with this simple model.
Input-Specific Spine Entry of Soma-Derived Vesl-1S Protein Conforms to Synaptic Tagging
Authors: Okada Daisuke , Ozawa Fumiko , Inokuchi Kaoru
Published: May 2009

Synaptic Tag Tagged

Input-dependent synaptic plasticity is critical for the reproducible activation of a specific neuronal assembly encoding a particular memory. The synaptic tagging hypothesis, which suggests how input specificity is maintained in late-phase synaptic plasticity, attempts to explain the persistence of long-term memory. However, it has been difficult to identify proteins that behave as the hypothesis predicts.

Okada
et al.

(p.
904
) investigated if the regulated spine entry of a late-phase-related somatically synthesized plasticity-related protein, Vesl-1S, works as a synaptic tag. Vesl-1S protein was carried from the soma to every dendrite and recruited into spines by synaptic activation in an input-specific manner. Spine entry was protein-synthesis independent, was NMDA receptor dependent, and had a persistent lifetime of activation. These results provide long-sought evidence for the input-specific capturing of a plasticity-related protein as postulated by the synaptic tagging hypothesis.
Stimulus Spending Looms Large as Obama Charts a Course for Science
Authors: Mervis Jeffrey
Published: May 2009

In President Barack Obama's $3.6 trillion budget request to Congress—his first since taking office in January—overall spending on research would creep up by 0.6%, to $59 billion, over the comparable appropriation for 2009.
‘Vengeance’ Bites Back At Jared Diamond
Authors: Balter Michael
Published: May 2009

Two tribesmen from Papua New Guinea are suing the prominent biologist over a popular magazine article about the human thirst for retribution.
Differential LiveMycobacterium tuberculosis-,M. bovisBCG-, Recombinant ESAT6-, and Culture Filtrate Protein 10-Induced Immunity in Tuberculosis
Authors: Hasan Zahra , Jamil Bushra , Ashraf Mussarat , Islam Muniba , Dojki Maqboola , Irfan Muhammad , Hussain Rabia
Published: May 2009

The high prevalence ofMycobacterium tuberculosismakes it imperative that immune responses to evaluate could be predictive of infection. We investigated liveMycobacterium- and recombinant antigen-induced cytokine and chemokine responses in patients with active tuberculosis (TB) compared with those of healthy controls from an area where TB is endemic (ECs).M. tuberculosis-,M. bovisBCG-, ESAT6-, and culture filtrate protein 10 (CFP10)-induced responses were determined in peripheral blood mononuclear cells from patients with pulmonary TB (n= 38) and ECs (n= 39). The levels of the cytokines gamma interferon (IFN-γ) and interleukin-10 (IL-10) and the chemokines CCL2, CCL3, and CXCL9 were measured. The levels ofM. tuberculosis- and BCG-induced IFN-γ secretion were significantly reduced (P= 0.002 andP< 0.01, respectively), while the amount of IL-10 induced by both virulent (P< 0.01) and avirulent (P= 0.002) mycobacteria was increased in patients with TB. The ESAT6-induced IFN-γ responses were increased in the patients with TB (P= 0.013) compared with those in the EC group. When tuberculin skin test (TST)-negative (TST−; induration, <10 mm) and TST-positive (TST+) donors were studied separately, both TST−and TST+individuals showed increased IFN-γ responses toM. tuberculosiscompared with the responses of the patients with TB (P= 0.037 andP= 0.006, respectively). However, only TST+ECs showed reduced IFN-γ responses to ESAT6 (P= 0.008) compared with the responses of the patients with TB. The levels ofM. tuberculosis-induced CCL2 (P= 0.006) and CXCL9 (P= 0.017) were greater in the patients with TB. The levels of CCL3 secretion in response toMycobacteriumand antigen stimulation were comparable between the two groups. While the levels of ESAT6-induced chemokines did not differ between the patients with TB and the ECs, the levels of CFP10-induced CCL2 (P= 0.01) and CXCL9 (P= 0.001) were increased in the patients. These data indicate differential host IFN-γ, CXCL9, and CCL2 responses to live mycobacteria and mycobacterial antigens and have implications for the identification of potential biomarkers of infection which could be used for the diagnosis of TB.
Comparison of Two Multiple-Locus Variable-Number Tandem-Repeat Analysis Methods for Molecular Strain Typing of Human
Brucella melitensis
Isolates from the Middle East
Authors: Tiller Rebekah V. , De Barun K. , Boshra Marie , Huynh Lynn Y. , Van Ert Matthew N. , Wagner David M. , Klena John , Mohsen T. S. , El-Shafie S. S. , Keim Paul , Hoffmaster Alex R. , Wilkins Patricia P. , Pimentel Guillermo
Published: May 2009

Brucella
species are highly monomorphic, with minimal genetic variation among species, hindering the development of reliable subtyping tools for epidemiologic and phylogenetic analyses. Our objective was to compare two distinct multiple-locus variable-number tandem-repeat analysis (MLVA) subtyping methods on a collection of 101
Brucella melitensis
isolates from sporadic human cases of brucellosis in Egypt (
n
= 83), Qatar (
n
= 17), and Libya (
n
= 1). A gel-based MLVA technique, MLVA-15
IGM
, was compared to an automated capillary electrophoresis-based method, MLVA-15
NAU
, with each MLVA scheme examining a unique set of variable-number tandem repeats. Both the MLVA
IGM
and MLVA
NAU
methods were highly discriminatory, resolving 99 and 101 distinct genotypes, respectively, and were able to largely separate genotypes from Egypt and Qatar. The MLVA-15
NAU
scheme presented higher strain-to-strain diversity in our test population than that observed with the MLVA-15
IGM
assay. Both schemes were able to genetically correlate some strains originating from the same hospital or region within a country. In addition to comparing the genotyping abilities of these two schemes, we also compared the usability, limitations, and advantages of the two MLVA systems and their applications in the epidemiological genotyping of human
B. melitensis
strains.
Genotypic Prediction of Human Immunodeficiency Virus Type 1 CRF02-AG Tropism
Authors: Raymond Stéphanie , Delobel Pierre , Mavigner Maud , Cazabat Michelle , Souyris Corinne , Encinas Stéphanie , Sandres-Sauné Karine , Pasquier Christophe , Marchou Bruno , Massip Patrice , Izopet Jacques
Published: May 2009

We assessed the performance of genotypic algorithms for predicting the tropism of human immunodeficiency virus type 1 coreceptor usage in 52 patients infected with the CRF02-AG subtype. The combined criteria of the 11/25 and net charge rules accurately detected CXCR4-using CRF02-AG viruses, whereas the Geno2pheno tool lacked sensitivity and the position-specific scoring matrix (PSSM) tool WebPSSM lacked specificity.
Characterization of a Highly Conserved Domain within the Severe Acute Respiratory Syndrome Coronavirus Spike Protein S2 Domain with Characteristics of a Viral Fusion Peptide
Authors: Madu Ikenna G. , Roth Shoshannah L. , Belouzard Sandrine , Whittaker Gary R.
Published: May 2009

Many viral fusion proteins are primed by proteolytic cleavage near their fusion peptides. While the coronavirus (CoV) spike (S) protein is known to be cleaved at the S1/S2 boundary, this cleavage site is not closely linked to a fusion peptide. However, a second cleavage site has been identified in the severe acute respiratory syndrome CoV (SARS-CoV) S2 domain (R797). Here, we investigated whether this internal cleavage of S2 exposes a viral fusion peptide. We show that the residues immediately C-terminal to the SARS-CoV S2 cleavage site SFIEDLLFNKVTLADAGF are very highly conserved across all CoVs. Mutagenesis studies of these residues in SARS-CoV S, followed by cell-cell fusion and pseudotyped virion infectivity assays, showed a critical role for residues L803, L804, and F805 in membrane fusion. Mutation of the most N-terminal residue (S798) had little or no effect on membrane fusion. Biochemical analyses of synthetic peptides corresponding to the proposed S2 fusion peptide also showed an important role for this region in membrane fusion and indicated the presence of α-helical structure. We propose that proteolytic cleavage within S2 exposes a novel internal fusion peptide for SARS-CoV S, which may be conserved across the
Coronaviridae
.
Features Distinguishing Epstein-Barr Virus Infections of Epithelial Cells and B Cells: Viral Genome Expression, Genome Maintenance, and Genome Amplification
Authors: Shannon-Lowe Claire , Adland Emily , Bell Andrew I. , Delecluse Henri-Jacques , Rickinson Alan B. , Rowe Martin
Published: May 2009

Epstein-Barr virus (EBV) is associated with malignant diseases of lymphoid and epithelial cell origin. The tropism of EBV is due to B-cell-restricted expression of CD21, the major receptor molecule for the virus. However, efficient infection of CD21
−
epithelial cells can be achieved via transfer from EBV-coated B cells. We compare and contrast here the early events following in vitro infection of primary B cells and epithelial cells. Using sensitive, quantitative reverse transcription-PCR assays for several latent and lytic transcripts and two-color immunofluorescence staining to analyze expression at the single cell level, we confirmed and extended previous reports indicating that the two cell types support different patterns of transcription. Furthermore, whereas infection of B cells with one or two copies of EBV resulted in rapid amplification of the viral genome to >20 copies per cell, such amplification was not normally observed after infection of primary epithelial cells or undifferentiated epithelial lines. In epithelial cells, EBNA1 expression was detected in only ca. 40% of EBER
+
cells, and the EBV genome was subsequently lost during prolonged culture. One exception was that infection of AGS, a gastric carcinoma line, resulted in maintenance of EBNA1 expression and amplification of the EBV episome. In contrast to B cells, where amplification of the EBV episome occurred even with a replication-defective BZLF1-knockout virus, amplification in AGS cells was dependent upon early lytic cycle gene expression. These data highlight the influence of the host cell on the outcome of EBV infection with regard to genome expression, amplification, and maintenance.
Evaluation of Recombinant Influenza Virus-Simian Immunodeficiency Virus Vaccines in Macaques
Authors: Sexton Amy , De Rose Robert , Reece Jeanette C. , Alcantara Sheilajen , Loh Liyen , Moffat Jessica M. , Laurie Karen , Hurt Aeron , Doherty Peter C. , Turner Stephen J. , Kent Stephen J. , Stambas John
Published: May 2009

There is an urgent need for human immunodeficiency virus (HIV) vaccines that induce robust mucosal immunity. Influenza A viruses (both H1N1 and H3N2) were engineered to express simian immunodeficiency virus (SIV) CD8 T-cell epitopes and evaluated following administration to the respiratory tracts of 11 pigtail macaques. Influenza virus was readily detected from respiratory tract secretions, although the infections were asymptomatic. Animals seroconverted to influenza virus and generated CD8 and CD4 T-cell responses to influenza virus proteins. SIV-specific CD8 T-cell responses bearing the mucosal homing marker β7 integrin were induced by vaccination of naïve animals. Further, SIV-specific CD8 T-cell responses could be boosted by recombinant influenza virus-SIV vaccination of animals with already-established SIV infection. Sequential vaccination with influenza virus-SIV recombinants of different subtypes (H1N1 followed by H3N2 or vice versa) produced only a limited boost in immunity, probably reflecting T-cell immunity to conserved internal proteins of influenza A virus. SIV challenge of macaques vaccinated with an influenza virus expressing a single SIV CD8 T cell resulted in a large anamnestic recall CD8 T-cell response, but immune escape rapidly ensued and there was no impact on chronic SIV viremia. Although our results suggest that influenza virus-HIV vaccines hold promise for the induction of mucosal immunity to HIV, broader antigen cover will be needed to limit cytotoxic T-lymphocyte escape.
Dissecting the Unique Nucleotide Specificity of Mimivirus Nucleoside Diphosphate Kinase
Authors: Jeudy Sandra , Lartigue Audrey , Claverie Jean-Michel , Abergel Chantal
Published: May 2009

The analysis of the
Acanthamoeba polyphaga
mimivirus genome revealed the first virus-encoded nucleoside diphosphate kinase (NDK), an enzyme that is central to the synthesis of RNA and DNA, ubiquitous in cellular organisms, and well conserved among the three domains of life. In contrast with the broad specificity of cellular NDKs for all types of ribo- and deoxyribonucleotides, the mimivirus enzyme exhibits a strongly preferential affinity for deoxypyrimidines. In order to elucidate the molecular basis of this unique substrate specificity, we determined the three-dimensional (3D) structure of the
Acanthamoeba polyphaga
mimivirus NDK alone and in complex with various nucleotides. As predicted from a sequence comparison with cellular NDKs, the 3D structure of the mimivirus enzyme exhibits a shorter Kpn loop, previously recognized as a main feature of the NDK active site. The structure of the viral enzyme in complex with various nucleotides also pinpointed two residue changes, both located near the active site and specific to the viral NDK, which could explain its stronger affinity for deoxynucleotides and pyrimidine nucleotides. The role of these residues was explored by building a set of viral NDK variants, assaying their enzymatic activities, and determining their 3D structures in complex with various nucleotides. A total of 26 crystallographic structures were determined at resolutions ranging from 2.8 Å to 1.5 Å. Our results suggest that the mimivirus enzyme progressively evolved from an ancestral NDK under the constraints of optimizing its efficiency for the replication of an AT-rich (73%) viral genome in a thymidine-limited host environment.
Late Devonian paleomagnetic age for the Polaris Mississippi Valley-type Zn–Pb deposit, Canadian Arctic Archipelago
Authors: Symons D. T. A. , Sangster D. F.
Published: May 2009

The Polaris Mississippi Valley-type (MVT) zinc–lead deposit is located in the Middle to Upper Ordovician Thumb Mountain Formation of the Cornwallis Fold Belt in the Canadian Arctic Archipelago. Paleomagnetic analysis was done on samples from 29 sites in the sphalerite–galena ore, the surrounding dolomitic envelope, and the adjacent host-rock limestones, using alternating-field and thermal step demagnetization, scanning electron microscopy with energy-dispersive analysis, and saturation isothermal remanente analyses. Excluding the modern viscous remanence component, the ore, dolomite alteration, and host limestones carry only a prefolding A remanent magnetization component that resides in single- and pseudosingle-domain magnetite, both as discrete grains and as inclusions in the MVT ore minerals. All evidence indicates that the mineralization and magnetization events were coeval. The mean magnetization direction of D = 145.8°, I = −31.1° (α95 = 5.9°, k = 26.2, N = 24) after tilt and a minor plunge correction gives a Late Devonian pole position of 28.6°N, 121.2°E (dp = 3.7°, dm = 6.6°, N = 24). The results indicate that the ore deposit was formed during the onset of the Ellesmerian Orogeny and tilted later in the orogeny.
Miocene tephra beds in the Cypress Hills of Saskatchewan, Canada
Authors: Vreeken Willem J. , Westgate John A.
Published: May 2009

Six rhyolitic tephra layers from ancient loess and related detritus in the Cypress Hills, Saskatchewan, represent separate volcanic eruptions from the Snake River Plain. Idaho, U.S.A. The weighted mean age and uncertainty of the youngest tephra bed is 8.3 ± 0.2 Ma, using the isothermal plateau fissiontrack technique on its hydrated glass shards. The loess that hosts five of these tephra beds extends across the Cypress Plain, which is the oldest (Middle Miocene) and highest depositional surface in the Interior Plains, and also occurs on four juxtaposed erosion surfaces. It appears that the first and maybe the second erosion surface began forming before 10 Ma, and that formation of the second, third, and fourth erosion surfaces was completed between 10 and 8.3 Ma.
Loomisella petryki, gen. nov., sp. nov., une algue udotéacée du Carbonifère, Formation de Mount Head, Alberta
Authors: Bergeron Mario , Mamet Bernard
Published: May 2009

The Loomis Member (Mount Head Formation) yields an abundant microflora of Viséan marine calcareous algae. A new udoteacean alga is recognized on the basis of the morphology of the tripartite lateral tubes. Tertiary fusiform filaments are disposed as hemispheric tufts and are attached by thin peduncles.
Some late Wenlock and Ludlow monograptid graptolites, Cornwallis Island, Arctic Canada
Authors: Lenz Alfred C.
Published: May 2009

Seven species of uncompressed latest Wenlock and Ludlow monograptid graptolites, isolated from calcareous concretions, are described and illustrated. The biostratigraphically important species "Pristiograptus" ludensis, of latest Wenlock age, and Saetograptus fritschi linearis and Monograptus ceratus, of mid-Ludlow age, are illustrated in uncompressed form for the first time. The remaining species described include Bohemograptus bohemicus tenuis, Colonograptus colonus, Saetograptus ex gr. chimaera, and Pristiograptus dalejensis, all of Ludlow age. The last-named species is the most common but is biostratigraphically long ranging.
Prevalence of a Trypanosome in Atlantic Cod (Gadus morhua) Especially in Relation to Stocks in the Newfoundland Area
Authors: Khan R. A. , Murphy J. , Taylor D.
Published: May 2009

A study was initiated to ascertain the prevalence of a trypanosome in Atlantic cod (Gadus morhua) especially in relation to stocks in the Newfoundland area and as an aid in management and conservation. Highest prevalences were recorded in fish taken off the Labrador coast (ICNAF divisions 2J and 3K, 94 and 90%, respectively). Trypanosomes were not as prevalent in fish collected from the northern Grand Bank (46%, division 3L) or from the southern Grand Bank (13 and 16%, divisions 3N and 3O, respectively). A further decrease in prevalence occurred among fish collected on the Flemish Cap (10%,, division 3M) and St. Pierre Bank (8%, subdivision 3Ps), while the lowest levels (4%) were apparent in cod taken from the Gulf of St. Lawrence (divisions 4R and 4S). Fish sampled at inshore localities reflected prevalences corresponding to some extent to offshore localities. Cod taken on coastal Labrador and from northern Newfoundland have a high prevalence of trypanosome infections while in the more easterly bays, intermediate levels occur. A conspicuous decrease in prevalence was apparent in a sample taken from the most easterly inshore locality (Portugal Cove) and from two others on the south coast of Newfoundland. Lowest prevalences were noted among fish taken at four inshore localities in the Gulf of St. Lawrence. These results, based on prevalences of infection, support conclusions from other studies that there are at least six stocks of cod in the Newfoundland area with some degree of mixing.Key words: trypanosome, prevalence, cod stocks, Newfoundland–Labrador, ICNAF
Spatial Distribution of Zooplankton and Phytoplankton in British Columbian Coastal Waters
Authors: Mackas David L. , Louttit Gregory C. , Austin Merelene J.
Published: May 2009

An automated sampling system was used to obtain continuous transects of near-surface temperature, chlorophyll fluorescence, and zooplankton abundance in Georgia Strait and off the southwest coast of Vancouver Island. At length scales shorter than ~10 km, correlation between phytoplankton and zooplankton was weak, while the strength and the sign of the larger scale correlation varied between sampling regions. In both regions, the large scale zooplankton patchiness could be contoured unambiguously and appeared to be oriented parallel to bathymetric contours. We also found evidence for smaller scale zooplankton concentrations over and near several shallow banks. Dissolved nutrient supply to the Continental Shelf off southwest Vancouver Island appears to be dominated by entrainment in the Georgia Strait/Juan de Fuca Strait estuarine system. The high nutrient supply allows a zone of high phytoplankton and zooplankton standing stock to develop along the outer coast of Vancouver Island.Key words: plankton, spatial distribution, British Columbian Shelf, inorganic nutrients
Gravel Bed Composition in Oregon Coastal Streams
Authors: Adams J. N. , Beschta R. L.
Published: May 2009

The amount of fine sediments (generally < 1 mm in diameter) in gravel bedded streams is often used as an indicator of habitat quality and also as a measure of the impact from accelerated sedimentation resulting from land disturbance. Five streams in the Oregon Coast Range were studied to evaluate temporal and spatial variability of streambed composition, as well as the factors affecting the amount of fine sediment within the bed. The amount of fine sediments (< 1 mm) contained in frozen streambed cores and expressed as a percentage (by weight) of the total sample proved highly variable in time and space. During a 19-mo sampling period, temporal variability was caused by an occasional flushing of fines from the gravel beds during high flows. Percent fines also varied greatly between streams, between locations in the same stream, and between locations in the same riffle. Streams on 21 Coast Range watersheds were sampled during summer low flow. The amount of fines averaged 19.4% for all watersheds and ranged from 10.6 to 29.4% for streams on undisturbed watersheds. Regression analysis indicated that the watershed slope, area, relief, and land use influenced the amount of fine sediment in the bed. Bed composition varied greatly between locations in the same stream with about 75% of the within-stream comparisons indicating a significant (α = 0.05) difference. Within a single stream, gravel bed composition correlated significantly with channel sinuosity and bank-full stage. Regression analysis and field observations suggested that road construction and logging operations can increase the amount of fines; however, such increases may be temporary if high flows flush the gravelsKey words: bed sediments, forest harvesting, Oregon Coast Range, sedimentation, spawning gravels, stream channels, water quality
An Examination of Cd, Cu, and Hg Concentrations in Livers of Northern Pike, Esox lucius, and White Sucker, Catostomus commersoni, from Five Lakes near a Base Metal Smelter at Flin Flon, Manitoba
Authors: McFarlane G. A. , Franzin W. G.
Published: May 2009

Concentrations of Cd, Cu, and Hg were examined in livers of northern pike (Esox lucius) and white sucker (Catostomus commersoni) from five lakes in the vicinity of, and receiving metal fallout from, a base metal smelter complex at Flin Flon, Manitoba. Concentrations of Cd in livers increased with increasing age in both species. Concentrations of Cu and Hg increased with age only in pike livers. The relationships of metal concentration to fish age were not consistent with the degree of contamination in lakes. Ca concentration of lake waters appeared to affect liver metal concentrations.Key words: Ca, Zn, Cu, Cd, Hg, white suckers, northern pike, bioaccumulation, smelter fallout.
Subitaneous and Resting Eggs of Copepods: Relative Rates of Clutch Production by Diaptomus leptopus
Authors: Watras C. J.
Published: May 2009

Because female Diaptomus leptopus carry subitaneous clutches longer than resting clutches, resting eggs can be produced at faster rates. Regression analysis of carrying times for 320 clutches produced at temperatures ranging from 12 to 24 °C indicated a consistent rate differential of 41%. This may facilitate colonization of the benthos by normally planktonic populations if pelagic conditions deteriorate.Key words: Copepoda. Diaptomus, reproduction, resting eggs, diapause, temperature effects
MELTING OF THE GLASS-LIKE 19-ATOM GOLD CLUSTER
Authors: REN SHI-WEI
Published: May 2009

In this paper, the melting behaviors of the glass-like cluster Au 19 are calculated and analyzed by using standard microcanonical molecular-dynamics simulations. The calculated results show a multi-step melting process. The first stage involves the majority of the surface atoms (14 atoms). An interesting phenomenon is that the minority of the surface atoms (4 atoms) are still in a solid-like state. The second stage involves all of the surface atoms. But there are two sites where the atoms stay for a relatively long time. The third stage corresponds to the frequent isomerizations involving all the surface atoms. The final stage consists of isomerization transitions involving all of the atoms, including the central atom of the cluster. The unique melting processes lead to the unique features of the caloric curve, the root-mean-square bond-length fluctuation, and the heat capacity of the glass-like Au 19.
Hordeivirus Replication, Movement, and Pathogenesis
Authors: Jackson Andrew O. , Lim Hyoun-Sub , Bragg Jennifer , Ganesan Uma , Lee Mi Yeon
Published: May 2009

The last Hordeivirus review appearing in this series 20 years ago focused on the comparative biology, relationships, and genome organization of members of the genus ( 68 ). Prior to the 1989 review, useful findings about the origin, disease occurrence, host ranges, and general biological properties of Barley stripe mosaic virus (BSMV) were summarized in three comprehensive reviews ( 26 , 67 , 107 ). Several recent reviews emphasizing contemporary molecular genetic findings also may be of interest to various readers ( 15 , 37 , 42 , 69 , 70 , 88 , 113 ). In the current review, we briefly reiterate the biological properties of the four members of the Hordeivirus genus and describe advances in our understanding of organization and expression of the viral genomes. We also discuss the infection processes and pathogenesis of the most extensively characterized Hordeiviruses and frame these advances in the broader context of viruses in other families that have encoded triple gene block proteins. In addition, an overview of recent advances in the use of BSMV for virus-induced gene silencing is presented.
Fungal Effector Proteins
Authors: Stergiopoulos Ioannis , de Wit Pierre J.G.M.
Published: May 2009

It is accepted that most fungal avirulence genes encode virulence factors that are called effectors. Most fungal effectors are secreted, cysteine-rich proteins, and a role in virulence has been shown for a few of them, including Avr2 and Avr4 of Cladosporium fulvum, which inhibit plant cysteine proteases and protect chitin in fungal cell walls against plant chitinases, respectively. In resistant plants, effectors are directly or indirectly recognized by cognate resistance proteins that reside either inside the plant cell or on plasma membranes. Several secreted effectors function inside the host cell, but the uptake mechanism is not yet known. Variation observed among fungal effectors shows two types of selection that appear to relate to whether they interact directly or indirectly with their cognate resistance proteins. Direct interactions seem to favor point mutations in effector genes, leading to amino acid substitutions, whereas indirect interactions seem to favor jettison of effector genes.
Central role of ceramide biosynthesis in body weight regulation, energy metabolism, and the metabolic syndrome
Authors: Yang Guang , Badeanlou Leylla , Bielawski Jacek , Roberts Amanda J. , Hannun Yusuf A. , Samad Fahumiya
Published: May 2009

Although obesity is associated with multiple features of the metabolic syndrome (insulin resistance, leptin resistance, hepatic steatosis, chronic inflammation, etc.), the molecular changes that promote these conditions are not completely understood. Here, we tested the hypothesis that elevated ceramide biosynthesis contributes to the pathogenesis of obesity and the metabolic syndrome. Chronic treatment for 8 wk of genetically obese ( ob/ob), and, high-fat diet-induced obese (DIO) mice with myriocin, an inhibitor of de novo ceramide synthesis, decreased circulating ceramides. Decreased ceramide was associated with reduced weight, enhanced metabolism and energy expenditure, decreased hepatic steatosis, and improved glucose hemostasis via enhancement of insulin signaling in the liver and muscle. Inhibition of de novo ceramide biosynthesis decreased adipose expression of suppressor of cytokine signaling-3 (SOCS-3) and induced adipose uncoupling protein-3 (UCP3). Moreover, ceramide directly induced SOCS-3 and inhibited UCP3 mRNA in cultured adipocytes suggesting a direct role for ceramide in regulation of metabolism and energy expenditure. Inhibition of de novo ceramide synthesis had no effect on adipose tumor necrosis factor-α (TNF-α) expression but dramatically reduced adipose plasminogen activator inhibitor-1 (PAI-1) and monocyte chemoattactant protein-1 (MCP-1). This study highlights a novel role for ceramide biosynthesis in body weight regulation, energy expenditure, and the metabolic syndrome.