bluuebunny/crossref_metadata_2025_split huggingface dataset:
A synthesis of subdisciplines: predator–prey interactions, and biodiversity and ecosystem functioning
Authors: Ives Anthony R. , Cardinale Bradley J. , Snyder William E. 
Published: December 2004

AbstractThe last 15 years has seen parallel surges of interest in two research areas that have rarely intersected: biodiversity and ecosystem functioning (BEF), and multispecies predator–prey interactions (PPI). Research addressing role of biodiversity in ecosystem functioning has focused primarily on single trophic‐level systems, emphasizing additive effects of diversity that manifest through resource partitioning and the sampling effect. Conversely, research addressing predator–prey interactions has focused on two trophic‐level systems, emphasizing indirect and non‐additive interactions among species. Here, we use a suite of consumer‐resource models to organize and synthesize the ways in which consumer species diversity affects the densities of both resources and consumer species. Specifically, we consider sampling effects, resource partitioning, indirect effects caused by intraguild interactions and non‐additive effects. We show that the relationship between consumer diversity and the density of resources and consumer species are broadly similar for systems with one vs. two trophic levels, and that indirect and non‐additive interactions generally do little more than modify the impacts of diversity established by the sampling effect and resource partitioning. The broad similarities between systems with one vs. two trophic levels argue for greater communication between researchers studying BEF, and researchers studying multispecies PPI.
Why environmental scientists are becoming Bayesians
Authors: Clark James S. 
Published: December 2004

AbstractAdvances in computational statistics provide a general framework for the high‐dimensional models typically needed for ecological inference and prediction. Hierarchical Bayes (HB) represents a modelling structure with capacity to exploit diverse sources of information, to accommodate influences that are unknown (or unknowable), and to draw inference on large numbers of latent variables and parameters that describe complex relationships. Here I summarize the structure of HB and provide examples for common spatiotemporal problems. The flexible framework means that parameters, variables and latent variables can represent broader classes of model elements than are treated in traditional models. Inference and prediction depend on two types of stochasticity, including (1)uncertainty, which describes our knowledge of fixed quantities, it applies to all ‘unobservables’ (latent variables and parameters), and it declines asymptotically with sample size, and (2)variability, which applies to fluctuations that are not explained by deterministic processes and does not decline asymptotically with sample size. Examples demonstrate how different sources of stochasticity impact inference and prediction and how allowance for stochastic influences can guide research.
The Case for Small Area Microdata
Authors: Tranmer Mark , Pickles Andrew , Fieldhouse Ed , Elliot Mark , Dale Angela , Brown Mark , Martin David , Steel David , Gardiner Chris 
Published: December 2004

SummaryCensus data are available in aggregate form for local areas and, through the samples of anonymized records (SARs), as samples of microdata for households and individuals. In 1991 there were two SAR files: a household file and an individual file. These have a high degree of detail on the census variables but little geographical detail, a situation that will be exacerbated for the 2001 SAR owing to the loss of district level geography on the individual SAR. The paper puts forward the case for an additional sample of microdata, also drawn from the census, that has much greater geographical detail. Small area microdata (SAM) are individual level records with local area identifiers and, to maintain confidentiality, reduced detail on the census variables. Population data from seven local authorities, including rural and urban areas, are used to define prototype samples of SAM. The rationale for SAM is given, with examples that demonstrate the role of local area information in the analysis of census data. Since there is a trade-off between the extent of local detail and the extent of detail on variables that can be made available, the confidentiality risk of SAM is assessed empirically. An indicative specification of the SAM is given, having taken into account the results of the confidentiality analysis.
The Random-Effects Proportional Hazards Model with Grouped Survival Data: A Comparison Between the Grouped Continuous and Continuation Ratio Versions
Authors: Grilli Leonardo 
Published: December 2004

SummaryWhen analysing grouped time survival data having a hierarchical structure it is often appropriate to assume a random-effects proportional hazards model for the latent continuous time and then to derive the corresponding grouped time model. There are two formally equivalent grouped time versions of the proportional hazards model obtained from different perspec-tives, known as the continuation ratio and the grouped continuous models. However, the two models require distinct estimation procedures and, more importantly, they differ substantially when extended to time-dependent covariates and/or non-proportional effects. The paper discusses these issues in the context of random-effects models, illustrating the main points with an application to a complex data set on job opportunities for a cohort of graduates.
The Ubiquitous Angle
Authors: Wood Graham R. , Saville David J. 
Published: December 2004

SummaryPreviously we used the geometry of n-dimensional space to derive the paired samples t-test and its p-value. In the present paper we describe the ‘ubiquitous’ application of these results to single degree of freedom linear model hypothesis tests. As examples, we derive the p- and t-values for the independent samples t-test, for testing a contrast in an analysis of variance and for testing the slope in a simple linear regression analysis. An angle θ in n-dimensional space is again pivotal in the development of the ideas. The relationships between p, t, θ, F and the correlation coefficient are also described by using a ‘statistical triangle’.
Robust, Accurate Confidence Intervals with a Weak Instrument: Quarter of Birth and Education
Authors: Imbens Guido W. , Rosenbaum Paul R. 
Published: December 2004

SummaryAn instrument or instrumental variable manipulates a treatment and affects the outcome only indirectly through its manipulation of the treatment. For instance, encouragement to exercise might increase cardiovascular fitness, but only indirectly to the extent that it increases exercise. If instrument levels are randomly assigned to individuals, then the instrument may permit consistent estimation of the effects caused by the treatment, even though the treatment assignment itself is far from random. For instance, one can conduct a randomized experiment assigning some subjects to ‘encouragement to exercise’ and others to ‘no encouragement’ but, for reasons of habit or taste, some subjects will not exercise when encouraged and others will exercise without encouragement; none-the-less, such an instrument aids in estimating the effect of exercise. Instruments that are weak, i.e. instruments that have only a slight effect on the treatment, present inferential problems. We evaluate a recent proposal for permutation inference with an instrumental variable in four ways: using Angrist and Krueger's data on the effects of education on earnings using quarter of birth as an instrument, following Bound, Jaeger and Baker in using simulated independent observations in place of the instrument in Angrist and Krueger's data, using entirely simulated data in which correct answers are known and finally using statistical theory to show that only permutation inferences maintain correct coverage rates. The permutation inferences perform well in both easy and hard cases, with weak instruments, as well as with long-tailed responses.
The Survival of Newly Founded Firms: A Case-Study into Varying-Coefficient Models
Authors: Kauermann Göran , Tutz Gerhard , Brüderl Josef 
Published: December 2004

SummaryThe success of a newly founded firm depends on various initial risk factors or start-up conditions such as the market that the business is aiming for, the experience and the age of the founder, the preparation before the launch, the financial frame and the legal form of the firm. These risk factors determine the chance of survival for the venture. However, the effects of these risk factors may change with time. Some effects may vanish whereas others remain constant. We analyse the survival of 1123 newly founded firms in the state of Bavaria, Germany. Our focus is on the investigation of time variation in the effects of risk factors. Time variation is tackled within the framework of varying-coefficient models, where time smoothly modifies the effects of risk factors. An important issue in our analysis is the separation of risk factors which have time-varying effects from those which have time constant effects. We make use of the Akaike criterion to separate these two types of risk factor.
A Comparison Study of Realtime Fatality Rates: Severe Acute Respiratory Syndrome in Hong Kong, Singapore, Taiwan, Toronto and Beijing, China
Authors: Yip Paul S. F. , Lam K. F. , Lau Eric H. Y. , Chau Pui-Hing , Tsang Kenneth W. , Chao Anne 
Published: December 2004

SummaryIn an outbreak of a completely new infectious disease like severe acute respiratory syndrome (SARS), estimation of the fatality rate over the course of the epidemic is of clinical and epidemiological importance. In contrast with the constant case fatality rate, a new measure, termed the ‘realtime’ fatality rate, is proposed for monitoring the new emerging epidemic at a population level. A competing risk model implemented via a counting process is used to estimate the realtime fatality rate in an epidemic of SARS. It can capture and reflect the time-varying nature of the fatality rate over the course of the outbreak in a timely and accurate manner. More importantly, it can provide information on the efficacy of a certain treatment and management policy for the disease. The method has been applied to the SARS data from the regions affected, namely Hong Kong, Singapore, Toronto, Taiwan and Beijing. The magnitudes and patterns of the estimated fatalities are virtually the same except in Beijing, which has a lower rate. It is speculated that the effect is linked to the different treatment protocols that were used. The standard estimate of the case fatality rate that was used by the World Health Organization has been shown to be unable to provide useful information to monitor the time-varying fatalities that are caused by the epidemic.
Integrating Intellectual Property Concepts into MIS Education: An Empirical Assessment*
Authors: Mykytyn Peter P. , Mykytyn Kathleen , Harrison David A. 
Published: December 2004

ABSTRACTThe evolving legal environment surrounding intellectual property (IP) and its impact on information systems, especially involving electronic commerce, and the type of education and training provided by management information systems (MIS) faculty to MIS students is a relationship that has not been investigated. Although organizations are confronted with IP infringement actions dealing with copyright, trademark, and their relationship to information systems, these issues are not adequately dealt with in MIS courses and programs today. These include improper posting of copyrighted material onto Web sites, improper use of metatags, and inappropriate deep linking and framing. Metatags, linking, and framing are often integral components of e‐commerce and web development coursework. Using the Theory of Planned Behavior (TPB), this study surveyed 122 MIS academics to ascertain their intentions to incorporate these IP concepts into their MIS courses. The results strongly support the TPB constructs regarding faculty members' intentions to incorporate these issues. Follow‐up contacts with a number of respondents also showed very strong support for academics actually incorporating these issues into their coursework.
Systemic Priming-Boosting Immunization with a Trivalent Plasmid DNA and Inactivated Murine Cytomegalovirus (MCMV) Vaccine Provides Long-Term Protection against Viral Replication following Systemic or Mucosal MCMV Challenge
Authors: Morello Christopher S. , Ye Ming , Hung Stephanie , Kelley Laura A. , Spector Deborah H. 
Published: December 2004

ABSTRACT

We previously demonstrated that vaccination of BALB/c mice with a pool of 13 plasmid DNAs (pDNAs) expressing murine cytomegalovirus (MCMV) genes followed by formalin-inactivated MCMV (FI-MCMV) resulted in complete protection against viral replication in the spleen and salivary glands following sublethal intraperitoneal (i.p.) challenge. Here, we found that following intranasal (i.n.) challenge, titers of virus in the lungs of the immunized mice were reduced approximately 1,000-fold relative to those for mock-immunized controls. We next sought to extend these results and to determine whether similar protection levels could be achieved by priming with a pool of three pDNAs containing three key plasmids (
IE1
,
M84
, and gB). We found that the three-pDNA priming elicited IE1- and
M84
-p65-specific CD8
+
T lymphocytes and, following FI-MCMV boost, high levels of virion-specific immunoglobulin G (IgG) and virus-neutralizing antibodies. When mice were i.n. challenged 4 months after the last boost, titers of virus in the lungs of immunized mice were reduced 1,000- to 2,000-fold from those for controls during the peak of viral replication. Additionally, titers of virus were either at or below the detection limits for the salivary glands, liver, and spleen of the majority of the immunized mice. Following sublethal i.p. challenge, virus was undetectable in all of the above target organs of the immunized mice. Virion-specific IgA in the lungs was consistently detected by day 6 post-i.n. challenge for the immunized mice and by day 14 for controls. These results demonstrate the immunity and high levels of protection of the priming-boosting vaccination against both systemic and mucosal challenge.
Cyclophilin Interactions with Incoming Human Immunodeficiency Virus Type 1 Capsids with Opposing Effects on Infectivity in Human Cells
Authors: Hatziioannou Theodora , Perez-Caballero David , Cowan Simone , Bieniasz Paul D. 
Published: December 2004

ABSTRACT
Cyclophilin A (CypA) is a peptidyl-prolyl isomerase that binds to the capsid protein (CA) of human immunodeficiency virus type 1 (HIV-1) and by doing so facilitates HIV-1 replication. Although CypA is incorporated into HIV-1 virions by virtue of CypA-Gag interactions that occur during virion assembly, in this study we show that the CypA-CA interaction that occurs following the entry of the viral capsid into target cells is the major determinant of CypA's effects on HIV-1 replication. Specifically, by using normal and CypA-deficient Jurkat cells, we demonstrate that the presence of CypA in the target and not the virus-producing cell enhances HIV-1 infectivity. Moreover, disruption of the CypA-CA interaction with cyclosporine A (CsA) inhibits HIV-1 infectivity only if the target cell expresses CypA. The effect of CsA on HIV-1 infection of human cells varies according to which particular cell line is used as a target, and CA mutations that confer CsA resistance and dependence exert their effects only if target cells, and not if virus-producing cells, are treated with CsA. The differential effects of CsA on HIV-1 infection in different human cells appear not to be caused by polymorphisms in the recently described retrovirus restriction factor TRIM5α. We speculate that CypA and/or CypA-related proteins affect the fate of incoming HIV-1 capsid either directly or by modulating interactions with unidentified host cell factors.
Novel Strategy for Generation and Titration of Recombinant Adeno-Associated Virus Vectors
Authors: Shiau Ai-Li , Liu Pu-Ste , Wu Chao-Liang 
Published: December 2004

ABSTRACT

Recombinant adeno-associated virus (rAAV) vectors have many advantages for gene therapeutic applications compared with other vector systems. Several methods that use plasmids or helper viruses have been reported for the generation of rAAV vectors. Unfortunately, the preparation of large-scale rAAV stocks is labor-intensive. Moreover, the biological titration of rAAV is still difficult, which may limit its preclinical and clinical applications. For this study, we developed a novel strategy to generate and biologically titrate rAAV vectors. A recombinant pseudorabies virus (PrV) with defects in its gD, gE, and thymidine kinase genes was engineered to express the AAV
rep
and
cap
genes, yielding PS virus, which served as a packaging and helper virus for the generation of rAAV vectors. PS virus was useful not only for generating high-titer rAAV vectors by cotransfection with an rAAV vector plasmid, but also for amplifying rAAV stocks. Notably, the biological titration of rAAV vectors was also feasible when cells were coinfected with rAAV and PS virus. Based on this strategy, we produced an rAAV that expresses prothymosin α (ProT). Expression of the ProT protein in vitro and in vivo mediated by rAAV/ProT gene transfer was detected by immunohistochemistry and a bioassay. Taken together, our results demonstrate that the PrV vector-based system is useful for generating rAAV vectors carrying various transgenes.
Severe Acute Respiratory Syndrome Coronavirus Infection of Golden Syrian Hamsters
Authors: Roberts Anjeanette , Vogel Leatrice , Guarner Jeannette , Hayes Norman , Murphy Brian , Zaki Sherif , Subbarao Kanta 
Published: December 2004

ABSTRACT
Small animal models are needed in order to evaluate the efficacy of candidate vaccines and antivirals directed against the severe acute respiratory syndrome coronavirus (SARS CoV). We investigated the ability of SARS CoV to infect 5-week-old Golden Syrian hamsters. When administered intranasally, SARS CoV replicates to high titers in the lungs and nasal turbinates. Peak replication in the lower respiratory tract was noted on day 2 postinfection (p.i.) and was cleared by day 7 p.i. Low levels of virus were present in the nasal turbinates of a few hamsters at 14 days p.i. Viral replication in epithelial cells of the respiratory tract was accompanied by cellular necrosis early in infection, followed by an inflammatory response coincident with viral clearance, focal consolidation in pulmonary tissue, and eventual pulmonary tissue repair. Despite high levels of virus replication and associated pathology in the respiratory tract, the hamsters showed no evidence of disease. Neutralizing antibodies were detected in sera at day 7 p.i., and mean titers at day 28 p.i. exceeded 1:400. Hamsters challenged with SARS CoV at day 28 p.i. were completely protected from virus replication and accompanying pathology in the respiratory tract. Comparing these data to the mouse model, SARS CoV replicates to a higher titer and for a longer duration in the respiratory tract of hamsters and is accompanied by significant pathology that is absent in mice. Viremia and extrapulmonary spread of SARS CoV to liver and spleen, which are seen in hamsters, were not detected in mice. The hamster, therefore, is superior to the mouse as a model for the evaluation of antiviral agents and candidate vaccines against SARS CoV replication.
Ebola Virus Glycoprotein Toxicity Is Mediated by a Dynamin-Dependent Protein-Trafficking Pathway
Authors: Sullivan Nancy J. , Peterson Mary , Yang Zhi-yong , Kong Wing-pui , Duckers Heinricus , Nabel Elizabeth , Nabel Gary J. 
Published: December 2004

ABSTRACT
Ebola virus infection causes a highly lethal hemorrhagic fever syndrome associated with profound immunosuppression through its ability to induce widespread inflammation and cellular damage. Though GP, the viral envelope glycoprotein, mediates many of these effects, the molecular events that underlie Ebola virus cytopathicity are poorly understood. Here, we define a cellular mechanism responsible for Ebola virus GP cytotoxicity. GP selectively decreased the expression of cell surface molecules that are essential for cell adhesion and immune function. GP dramatically reduced levels of αVβ3 without affecting the levels of α2β1 or cadherin, leading to cell detachment and death. This effect was inhibited in vitro and in vivo by brefeldin A and was dependent on dynamin, the GTPase. GP also decreased cell surface expression of major histocompatibility complex class I molecules, which alters recognition by immune cells, and this effect was also dependent on the mucin domain previously implicated in GP cytotoxicity. By altering the trafficking of select cellular proteins, Ebola virus GP inflicts cell damage and may facilitate immune escape by the virus.
Synchronized Infection of Cell Cultures by Magnetically Controlled Virus
Authors: Haim Hillel , Steiner Israel , Panet Amos 
Published: December 2004

ABSTRACT
To override the diffusion-limited adsorption step of viral infection, we magnetically synchronized cell attachment. Human immunodeficiency virus type 1-based lentivirus preparations were rendered magnetically reactive by association with magnetite nanoparticles, 50 nm in diameter. Application of a magnetic field resulted in immediate redistribution of the viral inoculum to the cell-associated state and completion of the productive adsorption process within 1 min. Independent of adsorption time, viral concentration, and diffusion rate, infection subsequently progressed by the receptor-mediated entry mechanism. Synchronization of this rate-limiting step of infection may now be applied to analyze isolated events in the viral replication sequence.
Interaction with Coxsackievirus and Adenovirus Receptor, but Not with Decay-Accelerating Factor (DAF), Induces A-Particle Formation in a DAF-Binding Coxsackievirus B3 Isolate
Authors: Milstone Aaron M. , Petrella JenniElizabeth , Sanchez Melissa D. , Mahmud Mariam , Whitbeck J. Charles , Bergelson Jeffrey M. 
Published: December 2004

ABSTRACT
Although many coxsackie B viruses interact with decay accelerating factor (DAF), attachment to DAF by itself is not sufficient to initiate infection. We examined the early events in infection that follow virus interaction with DAF, and with the coxsackievirus and adenovirus receptor (CAR). Interaction with soluble CAR in a cell-free system, or with CAR on the surfaces of transfected cells, induced the formation of A particles; interaction with soluble or cell surface DAF did not. The results suggest that CAR, but not DAF, is capable of initiating the conformational changes in the viral capsid that lead to release of viral nucleic acid.