bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tests are perfectly reliable
Authors: Lumsden J. 
Published: August 2011

All test items are perfectly reliable. The unreliability of test scores results solely from person fluctuations. The theory implies that: (1) test length effects are a sampling phenomenon; (2) person reliabilities can be compared from person characteristic curves; (3) all ICC for a unidimensional test have the same slope; (4) ICC are not necessarily invariant from one group to another; and (5) reliabilities of groups can be compared from ICC.A reliability coefficient of the theory is defined as the proportion of variance in obtained scores attributable to variance in average attribute level for subjects. Lower bounds for the classical reliability coefficient are also lower bounds for the new coefficient. Statistics calculated from this coefficient have no useful application.
Statistical analysis of discrete relational data
Authors: Wasserman Stanley , Iacobucci Dawn 
Published: August 2011

Social interaction data record the intensity of the relationship, or frequency of interaction, between two individual actors. Recent methods for analysing such data have treated these relational variables as continuous. A more appropriate method, described here, views these dyadic interactions as variables in multidimensional discrete cross‐classified arrays, thus permitting analysis by log‐linear models.These methods extend previous approaches to social interaction data, which were limited to binary relations, by focusing on discrete‐valued relations. Dyadic interactions, measured for a single discrete relational variable, are modelled stochastically using tendencies towards expansiveness (actor‐effects), popularity (partner‐effects) and reciprocity. Actor‐characteristic variables may be used to group actors into a substantive partition, thus simplifying the analysis and subsequent interpretations.
Estimation and application of latent variable models in categorical data analysis
Authors: Leung S. O. 
Published: August 2011

Bartholomew (1980, 1984a) has laid down a foundation for factor analysis based on latent variable models. Shea (1984, 1985) has provided computer programs for estimating one‐factor latent variable models when responses are binary or polytomous variables. However, the programs have limitations on number of variables and the sample size, which limits their applicability, especially when variables are polytomous. However, the more important limitation is that it is not possible to use two‐factor models when one‐factor models are not adequate.Here, we have gone further and successfully obtained maximum likelihood estimates for both the one‐factor and two‐factor latent variable models for binary and polytomous variables. The new algorithm is much faster because of careful and efficient programming. More importantly, generalization to high latent domensions is straightforward. Formal hypothesis testing is very difficult when variables are very large in number. However, we have shown in our examples that some interesting graphical interpretations can be made.
A hyperbolic cosine latent trait model for unfolding polytomous responses: Reconciling Thurstone and Likert methodologies
Authors: Andrich David 
Published: August 2011

In the 1920s, Thurstone articulated a theory for the measurement of social variables that involved two distinct steps: first constructing and operationalizing a linear continuum by locating statements according to their affective values; second measuring persons. The first step involved the pair‐comparison design and the cumulative response mechanism, the second step involved the direct‐response design (of the form Agree or Disagree) and the unfolding response mechanism. In the 1930s, Likert proposed a procedure that obviated the need for the first step and apparently permitted measuring persons from their responses to statements that were similar to those used by Thurstone, but which required a response that indicated degrees of intensity of the form Strongly Agree, Agree, Undecided, Disagree or Strongly Disagree. Furthermore, and in contrast to Thurstone, he implicitly used the cumulative mechanism, scoring the successive categories with successive integers and simply summing them to obtain a measurement for each person. The two procedures were considered to be distinct and alternative, and in general, this is still the perception with a number of matters still not reconciled between the two procedures.By resolving the Disagree response in the unfolding mechanism into its two constituent components, this paper presents an unfolding model for direct responses from first principles, and then generalises it to provide an unfolding model for polytomous responses of the Likert style. This model permits an understanding of those matters still not reconciled between the Thurstone and Likert approaches: First, Likert's success in using Thurstone‐like statements with the cumulative mechanism rather than the unfolding mechanism; second, the gap found between two clusters of locations when statements from a Likert‐style questionnaire are scaled using the Thurstone procedure; and third, the consistent problem with the middle category of Undecided in Likert‐style response formats.
Memory T-Cell Immune Response in Healthy Young Adults Vaccinated with Live Attenuated Influenza A (H5N2) Vaccine
Authors: Chirkova T. V. , Naykhin A. N. , Petukhova G. D. , Korenkov D. A. , Donina S. A. , Mironov A. N. , Rudenko L. G. 
Published: August 2011

ABSTRACTCellular immune responses of both CD4 and CD8 memory/effector T cells were evaluated in healthy young adults who received two doses of live attenuated influenza A (H5N2) vaccine. The vaccine was developed by reassortment of nonpathogenic avian A/Duck/Potsdam/1402-6/68 (H5N2) and cold-adapted A/Leningrad/134/17/57 (H2N2) viruses. T-cell responses were measured by standard methods of intracellular cytokine staining of gamma interferon (IFN-γ)-producing cells and a novel T-cell recognition of antigen-presenting cells by protein capture (TRAP) assay based on the trogocytosis phenomenon, namely, plasma membrane exchange between interacting immune cells. TRAP enables the detection of activated trogocytosis-positive T cells after virus stimulation. We showed that two doses of live attenuated influenza A (H5N2) vaccine promoted both CD4 and CD8 T-memory-cell responses in peripheral blood of healthy young subjects in the clinical study. Significant differences in geometric mean titers (GMTs) of influenza A (H5N2)-specific IFN-γ+cells were observed at day 42 following the second vaccination, while peak levels of trogocytosis+T cells were detected earlier, on the 21st day after the second vaccination. The inverse correlation of baseline levels compared to postvaccine fold changes in GMTs of influenza-specific CD4 and CD8 T cells demonstrated that baseline levels of these specific cells could be considered a predictive factor of vaccine immunogenicity.
Controlled Performance Evaluation of the DiversiLab Repetitive-Sequence-Based Genotyping System for Typing Multidrug-Resistant Health Care-Associated Bacterial Pathogens
Authors: Deplano Ariane , Denis Olivier , Rodriguez-Villalobos Hector , De Ryck Raf , Struelens Marc J. , Hallin Marie 
Published: August 2011

ABSTRACT

Fast, reliable, and versatile typing tools are essential to differentiate among related bacterial strains for epidemiological investigation and surveillance of health care-associated infection with multidrug-resistant (MDR) pathogens. The DiversiLab (DL) system is a semiautomated repetitive-sequence-based PCR system designed for rapid genotyping. The DL system performance was assessed by comparing its reproducibility, typeability, discriminatory power, and concordance with those of pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) and by assessing its epidemiological concordance on well-characterized MDR bacterial strains (
n
= 165). These included
vanA Enterococcus faecium
, extended-spectrum β-lactamase (ESBL)-producing strains of
Klebsiella pneumoniae
,
Escherichia coli
, and
Acinetobacter baumannii
, and ESBL- or metallo-β-lactamase (MBL)-producing
Pseudomonas aeruginosa
strains. The DL system showed very good performance for
E. faecium
and
K. pneumoniae
and good performance for other species, except for a discrimination index of <95% for
A. baumannii
and
E. coli
(93.9% and 93.5%, respectively) and incomplete concordance with MLST for
P. aeruginosa
(78.6%) and
E. coli
(97.0%). Occasional violations of MLST assignment by DL types were noted for
E. coli
. Complete epidemiological concordance was observed for all pathogens, as all outbreak-associated strains clustered in identical DL types that were distinct from those of unrelated strains. In conclusion, the DL system showed good to excellent performance, making it a reliable typing tool for investigation of outbreaks caused by study pathogens, even though it was generally less discriminating than PFGE analysis. For
E. coli
and
P. aeruginosa
, MLST cannot be reliably inferred from DL type due to phylogenetic group violation or discordance.
Functional Interactions between Polydnavirus and Host Cellular Innexins
Authors: Marziano N. K. , Hasegawa D. K. , Phelan P. , Turnbull M. W. 
Published: August 2011

ABSTRACT

Polydnaviruses are double-stranded DNA viruses associated with some subfamilies of ichneumonoid parasitoid wasps. Polydnavirus virions are delivered during wasp parasitization of a host, and virus gene expression in the host induces alterations of host physiology. Infection of susceptible host caterpillars by the polydnavirus
Campoletis sonorensis
ichnovirus (CsIV) leads to expression of virus genes, resulting in immune and developmental disruptions. CsIV carries four homologues of insect gap junction genes (innexins) termed vinnexins, which are expressed in multiple tissues of infected caterpillars. Previously, we demonstrated that two of these, VinnexinD and VinnexinG, form functional gap junctions in paired
Xenopus
oocytes. Here we show that VinnexinQ1 and VinnexinQ2, likewise, form junctions in this heterologous system. Moreover, we demonstrate that the vinnexins interact differentially with the Innexin2 orthologue of an ichnovirus host,
Spodoptera frugiperda
. Cell pairs coexpressing a vinnexin and Innexin2 or pairs in which one cell expresses a vinnexin and the neighboring cell Innexin2 assemble functional junctions with properties that differ from those of junctions composed of Innexin2 alone. These data suggest that altered gap junctional intercellular communication may underlie certain cellular pathologies associated with ichnovirus infection of caterpillar hosts.
Membrane Perturbation Elicits an IRF3-Dependent, Interferon-Independent Antiviral Response
Authors: Noyce Ryan S. , Taylor Kathryne , Ciechonska Marta , Collins Susan E. , Duncan Roy , Mossman Karen L. 
Published: August 2011

ABSTRACT
We previously found that enveloped virus binding and penetration are necessary to initiate an interferon-independent, IRF3-mediated antiviral response. To investigate whether membrane perturbations that accompany membrane fusion-dependent enveloped-virus entry are necessary and sufficient for antiviral-state induction, we utilized a reovirus fusion-associated small transmembrane (FAST) protein. Membrane disturbances during FAST protein-mediated fusion, in the absence of additional innate immune response triggers, are sufficient to elicit interferon-stimulated gene induction and establishment of an antiviral state. Using sensors of membrane disruption to activate an IRF3-dependent, interferon-independent antiviral state may provide cells with a rapid, broad-spectrum innate immune response to enveloped-virus infections.
Loss of Protease Dimerization Inhibition Activity of Darunavir Is Associated with the Acquisition of Resistance to Darunavir by HIV-1
Authors: Koh Yasuhiro , Aoki Manabu , Danish Matthew L. , Aoki-Ogata Hiromi , Amano Masayuki , Das Debananda , Shafer Robert W. , Ghosh Arun K. , Mitsuya Hiroaki 
Published: August 2011

ABSTRACT

Dimerization of HIV protease is essential for the acquisition of protease's proteolytic activity. We previously identified a group of HIV protease dimerization inhibitors, including darunavir (DRV). In the present work, we examine whether loss of DRV's protease dimerization inhibition activity is associated with HIV development of DRV resistance. Single amino acid substitutions, including I3A, L5A, R8A/Q, L24A, T26A, D29N, R87K, T96A, L97A, and F99A, disrupted protease dimerization, as examined using an intermolecular fluorescence resonance energy transfer (FRET)-based HIV expression assay. All recombinant HIV
NL4-3
-based clones with such a protease dimerization-disrupting substitution failed to replicate. A highly DRV-resistant
in vitro-
selected HIV variant and clinical HIV strains isolated from AIDS patients failing to respond to DRV-containing antiviral regimens typically had the V32I, L33F, I54M, and I84V substitutions in common in protease. None of up to 3 of the 4 substitutions affected DRV's protease dimerization inhibition, which was significantly compromised by the four combined substitutions. Recombinant infectious clones containing up to 3 of the 4 substitutions remained sensitive to DRV, while a clonal HIV variant with all 4 substitutions proved highly resistant to DRV with a 205-fold 50% effective concentration (EC
50
) difference compared to HIV
NL4-3
. The present data suggest that the loss of DRV activity to inhibit protease dimerization represents a novel mechanism contributing to HIV resistance to DRV. The finding that 4 substitutions in PR are required for significant loss of DRV's protease dimerization inhibition should at least partially explain the reason DRV has a high genetic barrier against HIV's acquisition of DRV resistance.
The Annual Cycle of Earth Radiation Budget from Clouds and the Earth’s Radiant Energy System (CERES) Data
Authors: Mlynczak Pamela E. , Smith G. Louis , Doelling David R. 
Published: August 2011

AbstractThe seasonal cycle of the Earth radiation budget is investigated by use of data from the Clouds and the Earth’s Radiant Energy System (CERES). Monthly mean maps of reflected solar flux and Earth-emitted flux on a 1° equal-angle grid are used for the study. The seasonal cycles of absorbed solar radiation (ASR), outgoing longwave radiation (OLR), and net radiation are described by use of principal components for the time variations, for which the corresponding geographic variations are the empirical orthogonal functions. Earth’s surface is partitioned into land and ocean for the analysis. The first principal component describes more than 95% of the variance in the seasonal cycle of ASR and the net radiation fluxes and nearly 90% of the variance of OLR over land. Because one term can express so much of the variance, principal component analysis is very useful to describe these seasonal cycles. The annual cycles of ASR are about 100 W m−2 over land and ocean, but the amplitudes of OLR are about 27 W m−2 over land and 15 W m−2 over ocean. The magnitude of OLR and its time lag relative to that of ASR are important descriptors of the climate system and are computed for the first principal components. OLR lags ASR by about 26 days over land and 42 days over ocean. The principal components are useful for comparing the observed radiation budget with that computed by a model.
Profiles of individually defined recovery of people with major psychiatric problems
Authors: van Gestel-Timmermans J. A. W. M. , Brouwers E. P. M. , Bongers I. L. , van Assen M. A. L. M. , van Nieuwenhuizen Ch. 
Published: August 2011

Background: Research on factors associated with individually defined recovery is limited. Several phases of recovery have been described in the literature. Individuals in these distinct phases have different characteristics and problems. Aims: To identify classes of people with major psychiatric problems who have comparable profiles of individually defined recovery, to relate these classes to the phases of recovery as described by Spaniol, Wewiorsky, Gagne, and Anthony (2002), and to associate the classes to demographic and psychiatric characteristics, and health-related variables. Methods: Data of 333 participants with major psychiatric problems were used. A latent class analysis was conducted on the mean scores of four proxy measures of recovery. Results: Three well-defined classes were found that differed on the recovery measures. The classes differed significantly on variables corresponding to Spaniol’s phases of recovery (Spaniol et al., 2002) and on health care utilization, health care needs and anxiety disorder, but not on demographic variables. Conclusions: It is possible to identify classes of people with major psychiatric problems who have comparable profiles of individually defined recovery that seem to correspond to phases of recovery. More knowledge of the characteristics of people in different phases of recovery will contribute to more fine-tuned and recovery-oriented health care.
Anti-C1q antibodies have higher correlation with flares of lupus nephritis than other serum markers
Authors: Akhter E , Burlingame RW , Seaman AL , Magder L , Petri M 
Published: August 2011

Objective. Autoantibodies are important in the diagnosis and classification of systemic lupus erythematosus (SLE), but whether they correlate with changes in disease activity within individual patients is controversial. We assessed the association between changes in SLE global and renal activity and changes in several autoantibodies and cell adhesion molecules in patients with SLE. Methods. Stored sera collected at two or three clinic visits from each of 49 SLE patients (91% female, 59% African-American, 31% Caucasian, 10% other ethnicity, 38% under 30 years, 41% between 30–44 years, and 21% 45–63 years) were analyzed. The visits were chosen to include one visit with proteinuria, and one or two without, for each patient. Global disease activity was measured by the Physician’s Global Assessment (PGA), SELENA-SLEDAI (SLE Disease Activity Index modified to exclude anti-dsDNA and complement) and renal activity assessed by urine protein (by urine dipstick) and Renal Activity Score. Sera were assayed for anti-C1q, anti-chromatin, anti-dsDNA, anti-ribosomal P, monocyte chemotactic protein-1 (MCP-1), vascular cell adhesion molecule (VCAM) intercellular adhesion molecule (ICAM) and complement. The associations between changes in disease activity and changes in biomarker levels were assessed. Results. In terms of global disease activity, anti-C1q had the highest association with the PGA ( p = 0.09) and was strongly associated with modified SELENA-SLEDAI ( p = 0.009). In terms of renal activity, anti-C1q had the highest association with proteinuria ( p = 0.079), and was strongly associated with Renal Activity Score ( p = 0.006). Conclusion. Anti-C1q performed the best of the potential biomarkers, being significantly associated with the modified SELENA-SLEDAI and with the Renal Activity Score. This study indicates the potential superior utility of anti-C1q over anti-dsDNA and other measures to track renal activity.
Identification of new IS711 insertion sites in Brucella abortus field isolates
Authors: Mancilla Marcos , Ulloa Marcos , López-Goñi Ignacio , Moriyón Ignacio , María Zárraga Ana 
Published: August 2011

Abstract

Background
Brucellosis is a zoonosis caused by Brucella spp., a group of highly homogeneous bacteria. The insertion sequence IS711 is characteristic of these bacteria, and occurs in variable numbers and positions, but always constant within a given species. This species-associated polymorphism is used in molecular typing and identification. Field isolates of B. abortus, the most common species infecting cattle, typically carry seven IS711 copies (one truncated). Thus far, IS711 transposition has only been shown in vitro and only for B. ovis and B. pinnipedialis, two species carrying a high number of IS711 copies, but never in other Brucella species, neither in vitro nor in field strains.

Results
We found several B. abortus strains isolated from milk and aborted fetuses that carried additional IS711 copies in two hitherto undescribed insertion sites: one in an intergenic region near to the 3' end of a putative lactate permease gene and the other interrupting the sequence of a marR transcriptional regulator gene. Interestingly, the second type of insertion was identified in isolates obtained repeatedly from the same herd after successive brucellosis outbreaks, an observation that proves the stability and virulence of the new genotype under natural conditions. Sequence analyses revealed that the new copies probably resulted from the transposition of a single IS711 copy common to all Brucella species sequenced so far.

Conclusions
Our results show that the replicative transposition of IS711 can occur under field conditions. Therefore, it represents an active mechanism for the emergence of genetic diversity in B. abortus thus contributing to intra-species genetic polymorphism.
Oral administration of a probiotic Lactobacillus modulates cytokine production and TLR expression improving the immune response against Salmonella enterica serovar Typhimurium infection in mice
Authors: Castillo Natalia A , Perdigón Gabriela , de Moreno de LeBlanc Alejandra 
Published: August 2011

AbstractBackgroundDiarrheal infections caused bySalmonella, are one of the major causes of childhood morbidity and mortality in developing countries.Salmonellacauses various diseases that range from mild gastroenteritis to enteric fever, depending on the serovar involved, infective dose, species, age and immune status of the host. Probiotics are proposed as an attractive alternative possibility in the prevention against this pathogen infection. Previously we demonstrated that continuousLactobacillus caseiCRL 431 administration to BALB/c mice before and after challenge withSalmonella entericaserovar Typhimurium (S. Typhimurium) decreased the severity ofSalmonellainfection. The aim of the present work was to deep into the knowledge about how this probiotic bacterium exerts its effect, by assessing its impact on the expression and secretion of pro-inflammatory (TNFα, IFNγ) and anti-inflammatory (IL-10) cytokines in the inductor and effector sites of the gut immune response, and analyzing toll-like receptor (TLR2, TLR4, TLR5 and TLR9) expressions in both healthy and infected mice.ResultsProbiotic administration to healthy mice increased the expression of TLR2, TLR4 and TLR9 and improved the production and secretion of TNFα, IFNγ and IL-10 in the inductor sites of the gut immune response (Peyer's patches). Post infection, the continuous probiotic administration, before and afterSalmonellachallenge, protected the host by modulating the inflammatory response, mainly in the immune effector site of the gut, decreasing TNFα and increasing IFNγ, IL-6 and IL-10 production in the lamina propria of the small intestine.ConclusionsThe oral administration ofL. caseiCRL 431 induces variations in the cytokine profile and in the TLRs expression previous and also after the challenge withS. Typhimurium. These changes show some of the immune mechanisms implicated in the protective effect of this probiotic strain againstS. Typhimurium, providing an alternative way to reduce the severity of the infection.