bluuebunny/crossref_metadata_2025 huggingface dataset:
A Comparison of Angoff and Bookmark Standard Setting Methods
Authors: Buckendahl Chad W. , Smith Russell W. , Impara James C. , Plake Barbara S.
Published: June 2006

This article presents a comparison of simplified variations on two prevalent methods, Angoff and Bookmark, for setting cut scores on educational assessments. The comparison is presented through an application with a Grade 7 Mathematics Assessment in a midwestem school district. Training and operational methods and procedures for each method are described in detail along with comparative results for the application. An alternative item ordering strategy for the Bookmark method that may increase its usability is also introduced. Although the Angoff method is more widely used, the Bookmark method has some promising features, specifically in educational settings. Teachers are able to focus on the expected performance of the “barely proficient” student without the additional challenge of estimating absolute item dificulty.
Detecting Multidimensionality Due to Curricular Differences
Authors: DeMars Christine E.
Published: June 2006

Data were generated to simulate multidimensionality resulting from including two or four subtopics on a test. Each item was dependent on an ability trait due to instruction and learning, which was the same across all items, as well as an ability trait unique to the subtopic of the test (such as biology on a general science test). The eigenvalues of the item correlation matrix and Yen's Q3 were not greatly influenced by multidimensionality under conditions where the responses of a large proportion of students shared the influence of common instruction across subtopics. In contrast, Stout's T procedure was effective at detecting this type of multidimensionality, unless the subtopic abilities were correlated.
A Comparative Study of Item Exposure Control Methods in Computerized Adaptive Testing
Authors: Chang Shun‐Wen , Ansley Timothy N.
Published: June 2006

This study compared the properties of five methods of item exposure control within the purview of estimating examinees’ abilities in a computerized adaptive testing (CAT) context. Each exposure control algorithm was incorporated into the item selection procedure and the adaptive testing progressed based on the CAT design established for this study. The merits and shortcomings of these strategies were considered under different item pool sizes and different desired maximum exposure rates and were evaluated in light of the observed maximum exposure rates, the test overlap rates, and the conditional standard errors of measurement. Each method had its advantages and disadvantages, but no one possessed all of the desired characteristics. There was a clear and logical trade‐off between item exposure control and measurement precision. The Stocking and Lewis conditional multinomial procedure and, to a slightly lesser extent, the Davey and Parshall method seemed to be the most promising considering all of the factors that this study addressed.
Construct Equivalence of Multiple‐Choice and Constructed‐Response Items: A Random Effects Synthesis of Correlations
Authors: Rodriguez Michael C.
Published: June 2006

A thorough search of the literature was conducted to locate empirical studies investigating the trait or construct equivalence of multiple‐choice (MC) and constructed‐response (CR) items. Of the 67 studies identified, 29 studies included 56 correlations between items in both formats. These 56 correlations were corrected for attenuation and synthesized to establish evidence for a common estimate of correlation (true‐score correlations). The 56 disattenuated correlations were highly heterogeneous. A search for moderators to explain this variation uncovered the role of the design characteristics of test items used in the studies. When items are constructed in both formats using the same stem (stem equivalent), the mean correlation between the two formats approaches unity and is significantly higher than when using non‐stem‐equivalent items (particularly when using essay‐type items). Construct equivalence, in part, appears to be a function of the item design method or the item writer's intent.
Methodology for Examining the Reliability of Group Mean Difference Scores
Authors: Brennan Robert L. , Yin Ping , Kane Michael T.
Published: June 2006

This article treats various procedures for examining the reliability of group mean difference scores, with particular emphasis on procedures from univariate and multivariate generalizability theory. Attention is given to both traditional norm‐referenced perspectives on reliability as well as criterion‐referenced perspectives that focus on error‐tolerance ratios and functions of them. The procedures discussed are illustrated using three cohorts of data for third‐ and fourth‐grade students in Iowa who took the Iowa Tests of Basic Skills in recent years. For these data, estimates of reliability for norm‐referenced decisions tend to be relatively low. By contrast, for criterion‐referenced decisions, estimates of reliability‐like coefficients based on error‐tolerance ratios tend to be noticeably larger.
Use of the Rasch IRT Model in Standard Setting: An Item‐Mapping Method
Authors: Wang Ning
Published: June 2006

This article provides both logical and empirical evidence to justify the use of an item‐mapping method for establishing passing scores for multiple‐choice licensure and certification examinations. After describing the item‐mapping standard‐setting process, the rationale and theoretical basis for this method are discussed, and the similarities and differences between the item‐mapping and the Bookmark methods are also provided. Empirical evidence supporting use of the item‐mapping method is provided by comparing results from four standard‐setting studies for diverse licensure and certification examinations. The four cut score studies were conducted using both the item‐mapping and the Angoff methods. Rating data from the four standard‐setting studies, using each of the two methods, were analyzed using item‐by‐rater random effects generalizability and dependability studies to examine which method yielded higher inter‐judge consistency. Results indicated that the item‐mapping method produced higher inter‐judge consistency and achieved greater rater agreement than the Angoff method.
Using Patterns of Summed Scores in Paper‐and‐Pencil Tests and Computer‐Adaptive Tests to Detect Misfitting Item Score Patterns
Authors: Meijer Rob R.
Published: June 2006

Two new methods have been proposed to determine unexpected sum scores on sub‐tests (testlets) both for paper‐and‐pencil tests and computer adaptive tests. A method based on a conservative bound using the hypergeometric distribution, denoted p, was compared with a method where the probability for each score combination was calculated using a highest density region (HDR). Furthermore, these methods were compared with the standardized log‐likelihood statistic with and without a correction for the estimated latent trait value (denoted as l*z and lz, respectively). Data were simulated on the basis of the one‐parameter logistic model, and both parametric and non‐parametric logistic regression was used to obtain estimates of the latent trait. Results showed that it is important to take the trait level into account when comparing subtest scores. In a nonparametric item response theory (IRT) context, on adapted version of the HDR method was a powerful alterative to p. In a parametric IRT context, results showed that l*z had the highest power when the data were simulated conditionally on the estimated latent trait level.
The Chain and Post‐Stratification Methods for Observed‐Score Equating: Their Relationship to Population Invariance
Authors: von Davier Alina A. , Holland Paul W. , Thayer Dorothy T.
Published: June 2006

The Non‐Equivalent‐groups Anchor Test (NEAT) design has been in wide use since at least the early 1940s. It involves two populations of test takers, P and Q, and makes use of an anchor test to link them. Two linking methods used for NEAT designs are those (a) based on chain equating and (b) that use the anchor test to post‐stratify the distributions of the two operational test scores to a common population (i.e., Tucker equating and frequency estimation). We show that, under different sets of assumptions, both methods are observed score equating methods and we give conditions under which the methods give identical results. In addition, we develop analogues of the Dorans and Holland (2000) RMSD measures of population invariance of equating methods for the NEAT design for both chain and post‐stratification equating methods.
Sensitivity of Linkings Between AP Multiple‐Choice Scores and Composite Scores to Geographical Region: An Illustration of Checking for Population Invariance
Authors: Yang Wen‐Ling
Published: June 2006

This application study investigates whether the multiple‐choice to composite linking functions that determine Advanced Placement Program exam grades remain invariant over subgroups defined by region. Three years of test data from an AP exam are used to study invariance across regions. The study focuses on two questions: (a) How invariant are grade thresholds across regions? and (b) Do the small sample sizes for some regional groups present particular problems for assessing thresholds invariance? The equatability index proposed by Dorans and Holland (2000) is employed to evaluate the invariance of the linking functions, and cross‐classification is used to evaluate the invariance of the composite cut scores. Overall, the linkings across regions seem to hold up reasonably well. Nevertheless, more exams need to be examined.
The Utility of Third International Mathematics and Science Study Scales in Predicting Students' State Examination Performance
Authors: Sofroniou Nick , Kellaghan Thomas
Published: June 2006

To examine the predictive utility of three scales provided in the released database of the Third International Mathematics and Science Study (TIMSS) (international plausible values, standardized percent correct score, and national Rasch score), information was obtained on the performance in state examinations in mathematics and science in 1996 (2,969 Grade 8 students) and in 1997 (2,898 Grade 7 students) of students in the Republic of Ireland who had participated in TIMSS in 1995. Performance on TIMSS was related to later performance in the state examinations using normal and nonparametric maximum likelihood (NPML) random effects models. In every case, standardized percent correct scores were found to be the best predictors of later performance, followed by national Rasch scores, and lastly, by international plausible values. The estimates for normal mixing distributions are close to those estimated by the NPML approach, lending support to the validity of estimates.
Constructing Rotating Item Pools for Constrained Adaptive Testing
Authors: Ariel Adelaide , Veldkamp Bernard P. , van der Linden Wim J.
Published: June 2006

Preventing items in adaptive testing from being over‐ or underexposed is one of the main problems in computerized adaptive testing. Though the problem of overexposed items can be solved using a probabilistic item‐exposure control method, such methods are unable to deal with the problem of underexposed items. Using a system of rotating item pools, on the other hand, is a method that potentially solves both problems. In this method, a master pool is divided into (possibly overlapping) smaller item pools, which are required to have similar distributions of content and statistical attributes. These pools are rotated among the testing sites to realize desirable exposure rates for the items. A test assembly model, motivated by Gulliksen's matched random subtests method, was explored to help solve the problem of dividing a master pool into a set of smaller pools. Different methods to solve the model are proposed. An item pool from the Law School Admission Test was used to evaluate the performances of computerized adaptive tests from systems of rotating item pools constructed using these methods.
Discovery of Trypanocidal Compounds by Whole Cell HTS of Trypanosoma brucei
Authors: Mackey Zachary B. , Baca Arthur M. , Mallari Jeremy P. , Apsel Beth , Shelat Anang , Hansell Elizabeth J. , Chiang Peter K. , Wolff Brian , Guy Kiplin R. , Williams Janice , McKerrow James H.
Published: June 2006

Chemotherapy against human African trypanosomiasis relies on four drugs that cause frequent and occasionally severe side‐effects. Because human African trypanosomiasis is a disease of poor people in Africa, the traditional market‐driven pathways to drug development are not available. One potentially rapid and cost‐effective approach to identifying and developing new trypanocidal drugs would be high throughput‐screening of existing drugs already approved for other uses, as well as clinical candidates in late development. We have developed an ATP‐bioluminescence assay that could be used to rapidly and efficiently screen compound libraries against trypanosomes in a high throughput‐screening format to validate this notion. We screened a collection of 2160 FDA‐approved drugs, bioactive compounds and natural products to identify hits that were cytotoxic to cultured Trypanosoma brucei at a concentration of 1 μm or less. This meant that any hit identified would be effective at a concentration readily achievable by standard drug dosing in humans. From the screen, 35 hits from seven different drug categories were identified. These included the two approved trypanocidal drugs, suramin and pentamidine, several other drugs suspected but never validated as trypanocidal, and 17 novel trypanocidal drugs.
Consenting to bio-risk: xenotransplantation and the law
Authors: Fovargue Sara
Published: June 2006

Research into alternative sources of organs for transplantation, including the use of organs from non-human genetically engineered animals, has occurred since the introduction of allotransplantation in the 1960s. Xenotransplantation is different from other developing genetic technologies because whilst the potential benefit is to the individual, the possible risks are to society as a whole. The risks include the transmission of unknown and currently indeterminable infectious diseases. This article explores whether the current regulator framework is able to address this issue and, in particular, whether ‘first-party’ consent to involvement in a clinical trial is a sufficient to protect third parties from harm. The competence of a xeno-recipient to consent is also considered, and it is suggested that, at the very least, public debate and participation in deciding whether clinical trials should be permitted must occur, because by allowing xenotransplant trials to help an individual, the risks will be borne by all.
Executioners, bystanders and victims: collective guilt, the legacy of denazification and the birth of twentieth-century transitional justice
Authors: O'Donnell Therese
Published: June 2006

‘We did not go into the streets when our Jewish friends were led away; we did not scream until we too were destroyed … We are guilty of being alive.’

Karl Jaspers The Question of German Guilt, p 66

The following scene as recounted by the English writer James Stern occurred in a German town one week after Germany's unconditional surrender in May 1945. A crowd is gathered around a series of photographs which though initially seeming to depict garbage instead reveal dead human bodies. Each photograph has a heading ‘WHO IS GUILTY?’. The spectators are silent, appearing hypnotised, and eventually retreat one by one. The placards are later replaced with clearer photographs and placards proclaiming ‘THIS TOWNISGUILTY! YOUARE GUILTY!’.
The
Xist
RNA Gene Evolved in Eutherians by Pseudogenization of a Protein-Coding Gene
Authors: Duret Laurent , Chureau Corinne , Samain Sylvie , Weissenbach Jean , Avner Philip
Published: June 2006

The
Xist
noncoding RNA is the key initiator of the process of X chromosome inactivation in eutherian mammals, but its precise function and origin remain unknown. Although
Xist
is well conserved among eutherians, until now, no homolog has been identified in other mammals. We show here that
Xist
evolved, at least partly, from a protein-coding gene and that the loss of protein-coding function of the proto-
Xist
coincides with the four flanking protein genes becoming pseudogenes. This event occurred after the divergence between eutherians and marsupials, which suggests that mechanisms of dosage compensation have evolved independently in both lineages.
A Nearly Modern Amphibious Bird from the Early Cretaceous of Northwestern China
Authors: You Hai-lu , Lamanna Matthew C. , Harris Jerald D. , Chiappe Luis M. , O'Connor Jingmai , Ji Shu-an , Lü Jun-chang , Yuan Chong-xi , Li Da-qing , Zhang Xing , Lacovara Kenneth J. , Dodson Peter , Ji Qiang
Published: June 2006

Three-dimensional specimens of the volant fossil bird
Gansus yumenensis
from the Early Cretaceous Xiagou Formation of northwestern China demonstrate that this taxon possesses advanced anatomical features previously known only in Late Cretaceous and Cenozoic ornithuran birds. Phylogenetic analysis recovers
Gansus
within the Ornithurae, making it the oldest known member of the clade. The Xiagou Formation preserves the oldest known ornithuromorph-dominated avian assemblage. The anatomy of
Gansus
, like that of other non-neornithean (nonmodern) ornithuran birds, indicates specialization for an amphibious life-style, supporting the hypothesis that modern birds originated in aquatic or littoral niches.
Adeno-Associated Virus Rep Protein-Mediated Inhibition of Transcription of the Adenovirus Major Late Promoter In Vitro
Authors: Needham Patrick G. , Casper John M. , Kalman-Maltese Vivian , Verrill Kristin , Dignam John David , Trempe James P.
Published: June 2006

Adeno-associated virus (AAV) is a human parvovirus that normally requires a helper virus such as adenovirus (Ad) for replication. The four AAV replication proteins (Rep78, Rep68, Rep52, and Rep40) are pleiotropic effectors of virus integration, replication, transcription, and virion assembly. These proteins exert effects on Ad gene expression and replication. In transient plasmid transfection assays, Rep proteins inhibit gene expression from a variety of transcription promoters. We have examined Rep protein-mediated inhibition of transcription of the Ad major late transcription promoter (AdMLP) in vitro. Rep78/68 are the strongest transcription suppressors and the purine nucleotide binding site in the Rep proteins, and by implication, the ATPase activity or conformational change induced by nucleotide binding is required for full repression. Rep52 has modest effects, and Rep40 exerts no significant effect on transcription. Rep78/68 and their N-terminal 225-residue domain bind to a 55-bp AdMLP DNA fragment in gel shift assays, suggesting that protein-DNA interactions are required for inhibition. This interaction was confirmed in DNase I protection assays and maps to a region extending from the TATA box to the transcription initiation site. Gel shift, DNase I, and chemical cross-linking assays with TATA box-binding protein (TBP) and Rep68 indicate that both proteins interact with each other and with the promoter at adjacent sites. The demonstration of Rep interaction with TBP and the AdMLP suggests that Rep78/68 alter the preinitiation complex of RNA polymerase II transcription. These observations provide new insight into the mechanism of Rep-mediated inhibition of gene expression.
High Pathogenicity of Wild-Type Measles Virus Infection in CD150 (SLAM) Transgenic Mice
Authors: Sellin Caroline I. , Davoust Nathalie , Guillaume Vanessa , Baas Dominique , Belin Marie-Françoise , Buckland Robin , Wild T. Fabian , Horvat Branka
Published: June 2006

Measles virus (MV) infection causes an acute childhood disease, associated in certain cases with infection of the central nervous system and development of a severe neurological disease. We have generated transgenic mice ubiquitously expressing the human protein SLAM (signaling lymphocytic activation molecule), or CD150, recently identified as an MV receptor. In contrast to all other MV receptor transgenic models described so far, in these mice infection with wild-type MV strains is highly pathogenic. Intranasal infection of SLAM transgenic suckling mice leads to MV spread to different organs and the development of an acute neurological syndrome, characterized by lethargy, seizures, ataxia, weight loss, and death within 3 weeks. In addition, in this model, vaccine and wild-type MV strains can be distinguished by virulence. Furthermore, intracranial MV infection of adult transgenic mice generates a subclinical infection associated with a high titer of MV-specific antibodies in the serum. Finally, to analyze new antimeasles therapeutic approaches, we created a recombinant soluble form of SLAM and demonstrated its important antiviral activity both in vitro and in vivo. Taken together, our results show the high susceptibility of SLAM transgenic mice to MV-induced neurological disease and open new perspectives for the analysis of the implication of SLAM in the neuropathogenicity of other morbilliviruses, which also use this molecule as a receptor. Moreover, this transgenic model, in allowing a simple readout of the efficacy of an antiviral treatment, provides unique experimental means to test novel anti-MV preventive and therapeutic strategies.
Efficient Expression of the Adeno-Associated Virus Type 5 P41 Capsid Gene Promoter in 293 Cells Does Not Require Rep
Authors: Ye Chaoyang , Qiu Jianming , Pintel David J.
Published: June 2006

Efficient expression of the adeno-associated virus type 5 (AAV5) P41 capsid gene promoter required adenovirus E1A and/or E1B; however, in contrast to what was observed for expression of the AAV2 capsid gene promoter (P40), neither adenovirus infection nor the large Rep protein was required. Although both the AAV2 and the AAV5 large Rep proteins efficiently bound the (GAGY)
3
Rep-binding element, the AAV5 large Rep protein transactivated transcription of the inducible AAV2 P40 promoter much less well than AAV2 large Rep. Differences in their activation potentials were mapped to the amino-terminal region of the proteins, and the poorly transactivating AAV5 Rep protein could competitively inhibit AAV2 Rep transactivation.
Structured Treatment Interruptions with Tenofovir Monotherapy for Simian Immunodeficiency Virus-Infected Newborn Macaques
Authors: Van Rompay Koen K. A. , Singh Raman P. , Heneine Walid , Johnson Jeffrey A. , Montefiori David C. , Bischofberger Norbert , Marthas Marta L.
Published: June 2006

We demonstrated previously that prolonged tenofovir treatment of infant macaques, starting early during infection with virulent simian immunodeficiency virus (SIVmac251), can lead to persistently low or undetectable viremia even after the emergence of mutants with reduced in vitro susceptibility to tenofovir as a result of a K65R mutation in reverse transcriptase; this control of viremia was demonstrated to be mediated by the generation of effective antiviral immune responses. To determine whether structured treatment interruptions (STI) can induce similar immunologic control of viremia, eight newborn macaques were infected with highly virulent SIVmac251 and started on a tenofovir STI regimen 5 days later. Treatment was withdrawn permanently at 33 weeks of age. All animals receiving STI fared much better than 22 untreated SIVmac251-infected infant macaques. However, there was a high variability among animals in the viral RNA set point after complete drug withdrawal, and none of the animals was able to achieve long-term immunologic suppression of viremia to persistently low levels. Early immunologic and viral markers in blood (including the detection of the K65R mutation) were not predictive of the viral RNA set point after drug withdrawal. These results, which reflect the complex interactions between drug resistance mutations, viral virulence, and drug- and immune-mediated inhibition of virus replication, highlight the difficulties associated with trying to develop STI regimens with predictable efficacy for clinical practice.
Mycovirus Cryphonectria Hypovirus 1 Elements Cofractionate with
trans
-Golgi Network Membranes of the Fungal Host
Cryphonectria parasitica
Authors: Jacob-Wilk Debora , Turina Massimo , Van Alfen Neal K.
Published: June 2006

The mycovirus cryphonectria hypovirus 1 (CHV1) causes proliferation of vesicles in its host,
Cryphonectria parasitica
, the causal agent of chestnut blight. These vesicles have previously been shown to contain both CHV1 genomic double-stranded RNA (dsRNA) and RNA polymerase activity. To determine the cellular origins of these virus-induced membrane structures, we compared the fractionation of several cellular and viral markers. Results showed that viral dsRNA, helicase, polymerase, and protease p29 copurify with
C. parasitica trans
-Golgi network (TGN) markers, suggesting that the virus utilizes the fungal TGN for replication. We also show that the CHV1 protease p29 associates with vesicle membranes and is resistant to treatments that would release peripheral membrane proteins. Thus, p29 behaves as an integral membrane protein of the vesicular fraction derived from the fungal TGN. Protease p29 was also found to be fully susceptible to proteolytic digestion in the absence of detergent and, thus, is wholly or predominantly on the cytoplasmic face of the vesicles. Fractionation analysis of p29 deletion variants showed that sequences in the C terminal of p29 mediate membrane association. In particular, the C-terminal portion of the protein (Met-135-Gly-248) is sufficient for membrane association and is enough to direct p29 to the TGN vesicles in the absence of other viral elements.
The Signal Peptide of the Ebolavirus Glycoprotein Influences Interaction with the Cellular Lectins DC-SIGN and DC-SIGNR
Authors: Marzi Andrea , Akhavan Armin , Simmons Graham , Gramberg Thomas , Hofmann Heike , Bates Paul , Lingappa Vishwanath R. , Pöhlmann Stefan
Published: June 2006

The C-type lectins DC-SIGN and DC-SIGNR (collectively referred to as DC-SIGN/R) bind to the ebolavirus glycoprotein (EBOV-GP) and augment viral infectivity. DC-SIGN/R strongly enhance infection driven by the GP of EBOV subspecies. Zaire (ZEBOV) but have a much less pronounced effect on infection mediated by the GP of EBOV subspecies. Sudan (SEBOV). For this study, we analyzed the determinants of the differential DC-SIGN/R interactions with ZEBOV- and SEBOV-GP. The efficiency of DC-SIGN engagement by ZEBOV-GP was dependent on the rate of GP incorporation into lentiviral particles, while appreciable virion incorporation of SEBOV-GP did not allow robust DC-SIGN/R usage. Forced incorporation of high-mannose carbohydrates into SEBOV-GP augmented the engagement of DC-SIGN/R to the levels observed with ZEBOV-GP, indicating that appropriate glycosylation of SEBOV-GP is sufficient for efficient DC-SIGN/R usage. However, neither signals for N-linked glycosylation unique to SEBOV- or ZEBOV-GP nor the highly variable and heavily glycosylated mucin-like domain modulated the interaction with DC-SIGN/R. In contrast, analysis of chimeric GPs identified the signal peptide as a determinant of DC-SIGN/R engagement. Thus, ZEBOV- but not SEBOV-GP was shown to harbor high-mannose carbohydrates, and GP modification with these glycans was controlled by the signal peptide. These results suggest that the signal peptide governs EBOV-GP interactions with DC-SIGN/R by modulating the incorporation of high-mannose carbohydrates into EBOV-GP. In summary, we identified the level of GP incorporation into virions and signal peptide-controlled glycosylation of GP as determinants of attachment factor engagement.
Cloning, Expression, and Functional Characterization of the Equine Herpesvirus 1 DNA Polymerase and Its Accessory Subunit
Authors: Loregian Arianna , Case Alessandro , Cancellotti Enrico , Valente Carlo , Marsden Howard S. , Palù Giorgio
Published: June 2006

We report the expression and characterization of the putative catalytic subunit (pORF30) and accessory protein (pORF18) of equine herpesvirus 1 DNA polymerase, which are encoded by open reading frames 30 and 18 and are homologous to herpes simplex virus type 1 UL30 and UL42, respectively. In vitro transcription-translation of open reading frames 30 and 18 generated proteins of 136 and 45 kDa, respectively. In vitro-expressed pORF30 possessed basal DNA polymerase activity that was stimulated by pORF18, as measured by DNA polymerase assays in vitro. Purified baculovirus-expressed pORF30 exhibited DNA polymerase activity similar to that of the in vitro-expressed protein, and baculovirus-expressed pORF18 could stimulate both nucleotide incorporation and long-chain DNA synthesis by pORF30 in a dose- and time-dependent manner. The salt optima for activity of both pORF30 and the holoenzyme were substantially different from those for other herpesvirus DNA polymerases. As demonstrated by yeast two-hybrid assays, pORF30 and pORF18 could physically interact, most likely with a 1:1 stoichiometry. Finally, by mutational analysis of the 1,220-residue pORF30, we demonstrated that the extreme C terminus of pORF30 is important for physical and functional interaction with the accessory protein, as reported for UL30 and other herpesvirus DNA polymerases. In addition, a C-proximal region of pORF30, corresponding to residues 1114 to 1172, is involved in binding to, and stimulation by, pORF18. Taken together, the results indicate that pORF30 and pORF18 are the equine herpesvirus 1 counterparts of herpes simplex virus type 1 UL30 and UL42 and share many, but not all, of their characteristics.
Inhibition of Protein Trafficking by Coxsackievirus B3: Multiple Viral Proteins Target a Single Organelle
Authors: Cornell Christopher T. , Kiosses William B. , Harkins Stephanie , Whitton J. Lindsay
Published: June 2006

Despite replicating to very high titers, coxsackieviruses do not elicit strong CD8 T-cell responses, perhaps because antigen presentation is inhibited by virus-induced disruption of host protein trafficking. Herein, we evaluated the effects of three viral nonstructural proteins (2B, 2BC, and 3A) on intracellular trafficking. All three of these proteins inhibited secretion, to various degrees, and directly associated with the Golgi complex, causing trafficking proteins to accumulate in this compartment. The 3A protein almost completely ablated trafficking and secretion, by moving rapidly to the Golgi, and causing its disruption. Using an alanine-scanning 3A mutant, we show that Golgi targeting and disruption can be uncoupled. Thus, coxsackieviruses rely on the combined effects of several gene products that target a single cellular organelle to successfully block protein secretion during an infection. These findings have implications for viral pathogenesis.
Ep-CAM expression in pancreatic and ampullary carcinomas: frequency and prognostic relevance
Authors: Fong D , Steurer M , Obrist P , Barbieri V , Margreiter R , Amberger A , Laimer K , Gastl G , Tzankov A , Spizzo G
Published: June 2006

Aims:

Pancreatic adenocarcinoma is an aggressive gastrointestinal malignancy with only a few long-term survivors even after radical surgery. Patients with ampullary cancer have a better prognosis but adjuvant therapy needs further improvement. Epithelial cell adhesion molecule (Ep-CAM) is strongly expressed in a variety of epithelial cancers and represents a promising target for immunological tumour therapy. Thus, the aim of this study was to investigate Ep-CAM expression and its potential prognostic impact in pancreatic and ampullary carcinomas.

Methods:

Ep-CAM expression was investigated retrospectively by immunohistochemistry in paraffin-embedded primary tumour tissue samples from a series of consecutive patients with pancreatic (n = 153) and ampullary cancer (n = 34).

Results:

Ep-CAM overexpression was observed in 85 of 153 pancreatic cancer specimens (56%) and in 29 of 34 ampullary cancer samples (85%). Overall, Ep-CAM failed to be an independent prognostic marker. However, subgroup analyses showed that Ep-CAM overexpression correlated with shorter overall survival among patients with ampullary cancer and advanced stage pancreatic cancer. In the latter subgroup, survival gradually worsened with increasing Ep-CAM scores. Furthermore, in ampullary cancer, Ep-CAM overexpression was found to correlate with tumour stage.

Conclusions:

Ep-CAM overexpression was detectable in the majority of cases with pancreatic and ampullary cancer. Therefore, Ep-CAM represents an attractive target for immune-based therapeutic interventions in these tumour entities. However, the prognostic value of Ep-CAM overexpression remains undetermined.
MIXED ALGORITHMS IN THE ISING MODEL ON DIRECTED BARABÁSI–ALBERT NETWORKS
Authors: LIMA F. W. S.
Published: June 2006

On directed Barabási–Albert networks with two and seven neighbours selected by each added site, the Ising model does not seem to show a spontaneous magnetisation. Instead, the decay time for flipping of the magnetisation follows an Arrhenius law for Metropolis and Glauber algorithms, but for Wolff cluster flipping the magnetisation decays exponentially with time. On these networks the magnetisation behaviour of the Ising model, with Glauber, HeatBath, Metropolis, Wolf or Swendsen–Wang algorithm competing against Kawasaki dynamics, is studied by Monte Carlo simulations. We show that the model exhibits the phenomenon of self-organisation (= stationary equilibrium) defined in Ref. 8 when Kawasaki dynamics is not dominant in its competition with Glauber, HeatBath and Swendsen–Wang algorithms. Only for Wolff cluster flipping the magnetisation, this phenomenon occurs after an exponentially decay of magnetisation with time. The Metropolis results are independent of competition. We also study the same process of competition described above but with Kawasaki dynamics at the same temperature as the other algorithms. The obtained results are similar for Wolff cluster flipping, Metropolis and Swendsen–Wang algorithms but different for HeatBath.
NUCLEAR FUEL DEPLETION ANALYSIS USING MATLAB SOFTWARE
Authors: FAGHIHI F. , NEMATOLLAHI M. R.
Published: June 2006

Coupled first order IVPs are frequently used in many parts of engineering and sciences. In this article, we presented a code including three computer programs which are joint with the Matlab software to solve and plot the solutions of the first order coupled stiff or non-stiff IVPs. Some engineering and scientific problems related to IVPs are given and fuel depletion (production of the239Pu isotope) in a Pressurized Water Nuclear Reactor (PWR) are computed by the present code.
EXPLICIT EIGHTH ORDER TWO-STEP METHODS WITH NINE STAGES FOR INTEGRATING OSCILLATORY PROBLEMS
Authors: TSITOURAS Ch.
Published: June 2006

We present a new explicit hybrid two step method for the solution of second order initial value problem. It costs only nine function evaluations per step and attains eighth algebraic order so it is the cheapest in the literature. Its coefficients are chosen to reduce amplification and phase errors. Thus the method is well suited for facing problems with oscillatory solutions. After implementing a MATLAB program, we proceed with numerical tests that justify our effort.
MOTOR SCHEMA-BASED CELLULAR AUTOMATON MODEL FOR PEDESTRIAN DYNAMICS
Authors: WENG WENGUO , HASEMI YUJI , FAN WEICHENG
Published: June 2006

A new cellular automaton model for pedestrian dynamics based on motor schema is presented. Each pedestrian is treated as an intelligent mobile robot, and motor schemas including move-to-goal, avoid-away and avoid-around drive pedestrians to interact with their environment. We investigate the phenomenon of many pedestrians with different move velocities escaping from a room. The results show that the pedestrian with high velocity have predominance in competitive evacuation, if we only consider repulsion from or avoiding around other pedestrians, and interaction with each other leads to disordered evacuation, i.e., decreased evacuation efficiency. Extensions of the model using learning algorithms for controlling pedestrians, i.e., reinforcement learning, neural network and genetic algorithms, etc. are noted.
SOLUTION OF PRIDE'S EQUATIONS THROUGH POTENTIALS
Authors: PLYUSHCHENKOV BORIS D. , TURCHANINOV VICTOR I.
Published: June 2006

In 1994, S. Pride offered a system of equations describing interdependent propagation of acoustic and electromagnetic (EM) fields in porous media saturated by a fluid electrolyte (electrokinetic effect). We proved that the displacement vectors of frame and of pore fluid can be represented as a linear combinations of gradients of two scalar potentials and rotors of two vector potentials provided the coefficients of Pride's equations are independent of spatial coordinates. Each of these potentials satisfies Helmholtz equation with appropriate complex velocity. This representation underlies the computer code created by us for exploring borehole acoustics logging problems in axial-symmetric radially layered medium. Noteworthy, layers can be of any of the following types: uniform porous medium saturated by fluid electrolyte, uniform nonporous elastic medium, compressible nonviscous fluid or compressible viscous fluid. Results of numerical experiments are presented and discussed. The most important of them is that the back influence on acoustic disturbance of EM field excited by this disturbance is negligibly small in usually used frequency band and for realistic formation parameters. The mechanism of generation and propagation of different types of EM waves during acoustic logging is discussed as well.
Loss of cortical actin filaments in insulin-resistant skeletal muscle cells impairs GLUT4 vesicle trafficking and glucose transport
Authors: McCarthy Alicia M. , Spisak Kristen O. , Brozinick Joseph T. , Elmendorf Jeffrey S.
Published: June 2006

Study has demonstrated an essential role of cortical filamentous actin (F-actin) in insulin-regulated glucose uptake by skeletal muscle. Here, we tested whether perturbations in F-actin contributed to impaired insulin responsiveness provoked by hyperinsulinemia. In L6 myotubes stably expressing GLUT4 that carries an exofacial myc-epitope tag, acute insulin stimulation (20 min, 100 nM) increased GLUT4myc translocation and glucose uptake by ∼2-fold. In contrast, a hyperinsulinemic state, induced by inclusion of 5 nM insulin in the medium for 12 h decreased the ability of insulin to stimulate these processes. Defects in insulin signaling did not readily account for the observed disruption. In contrast, hyperinsulinemia reduced cortical F-actin. This occurred concomitant with a loss of plasma membrane phosphatidylinositol 4,5-bisphosphate (PIP2), a lipid involved in cytoskeletal regulation. Restoration of plasma membrane PIP2 in hyperinsulinemic cells restored F-actin and insulin responsiveness. Consistent with these in vitro observations suggesting that the hyperinsulinemic state negatively affects cortical F-actin structure, epitrochlearis skeletal muscle from insulin-resistant hyperinsulinemic Zucker fatty rats displayed a similar loss of F-actin structure compared with that in muscle from lean insulin-sensitive littermates. We propose that a component of insulin-induced insulin resistance in skeletal muscle involves defects in PIP2/F-actin structure essential for insulin-regulated glucose transport.
Effect of complete protein 4.1R deficiency on ion transport properties of murine erythrocytes
Authors: Rivera Alicia , De Franceschi Lucia , Peters Luanne L. , Gascard Philippe , Mohandas Narla , Brugnara Carlo
Published: June 2006

Moderate hemolytic anemia, abnormal erythrocyte morphology (spherocytosis), and decreased membrane stability are observed in mice with complete deficiency of all erythroid protein 4.1 protein isoforms (4.1−/−; Shi TS et al. J Clin Invest 103: 331, 1999). We have examined the effects of erythroid protein 4.1 (4.1R) deficiency on erythrocyte cation transport and volume regulation. 4.1−/− mice exhibited erythrocyte dehydration that was associated with reduced cellular K and increased Na content. Increased Na permeability was observed in these mice, mostly mediated by Na/H exchange with normal Na-K pump and Na-K-2Cl cotransport activities. The Na/H exchange of 4.1−/− erythrocytes was markedly activated by exposure to hypertonic conditions (18.2 ± 3.2 in 4.1−/− vs. 9.8 ± 1.3 mmol/1013 cell × h in control mice), with an abnormal dependence on osmolality (EC50 = 417 ± 42 in 4.1−/− vs. 460 ± 35 mosmol/kgH2O in control mice), suggestive of an upregulated functional state. While the affinity for internal protons was not altered (K0.5 = 489.7 ± 0.7 vs. 537.0 ± 0.56 nM in control mice), the Vmax of the H-induced Na/H exchange activity was markedly elevated in 4.1−/− erythrocytes ( Vmax 91.47 ± 7.2 compared with 46.52 ± 5.4 mmol/1013 cell × h in control mice). Na/H exchange activation by okadaic acid was absent in 4.1−/− erythrocytes. Altogether, these results suggest that erythroid protein 4.1 plays a major role in volume regulation and physiologically downregulates Na/H exchange in mouse erythrocytes. Upregulation of the Na/H exchange is an important contributor to the elevated cell Na content of 4.1−/− erythrocytes.
Claudins 6, 9, and 13 are developmentally expressed renal tight junction proteins
Authors: Abuazza Ghazala , Becker Amy , Williams Scott S. , Chakravarty Sumana , Truong Hoang-Trang , Lin Fangming , Baum Michel
Published: June 2006

The adult proximal tubule is a low-resistance epithelium where there are high rates of both active transcellular and passive paracellular NaCl transport. We have previously demonstrated that the neonatal rabbit and rat proximal tubule have substantively different passive paracellular transport properties than the adult proximal tubule, which results in a maturational change in the paracellular passive flux of ions. Neonatal proximal tubules have a higher PNa/PClratio and lower chloride and bicarbonate permeabilities than adult proximal tubules. Claudins are a large family of proteins which are the gate keepers of the paracellular pathway, and claudin isoform expression determines the permeability characteristics of the paracellular pathway. Previous studies have shown that claudins 1, 2, 3, 4, 5, 7, 8, 10, 11, 12, 15, and 16 are expressed in the adult mouse kidney. To determine whether there are developmental claudin isoforms, we compared the claudin isoforms present in the neonatal and adult kidney using RT-PCR to detect mRNA of claudin isoforms. Claudin 6, claudin 9, and claudin 13 were either not expressed or barely detectable in the adult mouse kidney using traditional PCR, but were expressed in the neonatal mouse kidney. Using real-time RT-PCR, we were able to detect a low level of claudin 6 mRNA expression in the adult kidney compared with the neonate, but claudin 9 and claudin 13 were only detected in the neonatal kidney. There was the same maturational decrease in these claudin proteins with Western blot analysis. Immunohistochemistry showed high levels of expression of claudin 6 in neonatal proximal tubules, thick ascending limb, distal convoluted tubules, and collecting ducts in a paracellular distribution but there was no expression of claudin 6 in the adult kidney. Using real-time RT-PCR claudin 6 and 9 mRNA were present in 1-day-old proximal convoluted tubules and were virtually undetectable in proximal convoluted tubules from adults. Claudin 13 was not detectable in neonatal or adult proximal convoluted tubules. In summary, we have identified developmentally expressed claudin isoforms, claudin 6, claudin 9, and claudin 13. These paracellular proteins may play a role in the maturational changes in paracellular permeability.
Parasternal intercostal muscle remodeling in severe chronic obstructive pulmonary disease
Authors: Levine Sanford , Nguyen Taitan , Friscia Michael , Zhu Jianliang , Szeto Wilson , Kucharczuk John C. , Tikunov Boris A. , Rubinstein Neal A. , Kaiser Larry R. , Shrager Joseph B.
Published: June 2006

Studies in experimental animals indicate that chronic increases in neural drive to limb muscles elicit a fast-to-slow transformation of fiber-type proportions and myofibrillar proteins. Since neural drive to the parasternal intercostal muscles (parasternals) is chronically increased in patients with severe chronic obstructive pulmonary diseases (COPDs), we carried out the present study to test the hypothesis that the parasternals of COPD patients exhibit an increase in the proportions of both slow fibers and slow myosin heavy chains (MHCs). Accordingly, we obtained full thickness parasternal muscle biopsies from the third interspace of seven COPD patients (mean ± SE age: 59 ± 4 yr) and seven age-matched controls (AMCs). Fiber typing was done by immunohistochemistry, and MHC proportions were determined by SDS-PAGE followed by densitometry. COPD patients exhibited higher proportions of slow fibers than AMCs (73 ± 4 vs. 51 ± 3%; P < 0.01). Additionally, COPD patients exhibited higher proportions of slow MHC than AMCs (56 ± 4 vs. 46 ± 4%, P < 0.04). We conclude that the parasternal muscles of patients with severe COPD exhibit a fast-to-slow transformation in both fiber-type and MHC proportions. Previous workers have demonstrated that remodeling of the external intercostals, another rib cage inspiratory muscle, elicited by severe COPD is characterized by a slow-to-fast transformation in both fiber types and MHC isoform proportions. The physiological significance of this difference in remodeling between these two inspiratory rib cage muscles remains to be elucidated.
Morphology and Physiology of the Cerebellar Vestibulolateral Lobe Pathways Linked to Oculomotor Function in the Goldfish
Authors: Straka Hans , Beck James C. , Pastor Angel M. , Baker Robert
Published: June 2006

Intracellular recording and single-cell labeling were combined to investigate the oculomotor circuitry of the goldfish cerebellar vestibulolateral lobe, consisting of the eminentia granularis (Egr) and caudal lobe. Purkinje cells exhibiting highly conserved vertebrate electrophysiological and morphological properties provide the direct output from the caudal lobe to the vestibular nuclei. Biocytin labeling of the Egr distinguished numerous hindbrain precerebellar sources that could be divided into either putative mechano- or vestibulosensitive nuclei based on cellular location and axon trajectories. Precerebellar neurons in a hindbrain nucleus, called Area II, were electrophysiologically characterized after antidromic activation from the Egr (>50% bilateral) and their morphology analyzed after intracellular biocytin labeling ( n = 28). Bipolar spindle-shaped somas ranged widely in size with comparably scaled dendritic arbors exhibiting largely closed field configuration. Area II neurons (85%) projected to the ipsilateral Egr with most (93%) sending a collateral through the cerebellar commissure to the contralateral Egr; however, 15% projected to the contralateral Egr by crossing in the ventral hindbrain. Axon terminals in the vestibular nucleus were the only collaterals within the hindbrain. Every Area II neuron received a disynaptic EPSP after contralateral horizontal canal nerve stimulation and a disynaptic IPSP, preceded by a small EPSP (>50%), after ipsilateral activation. Vestibular synaptic potentials were of varying shape/amplitude, unrelated to neuron location in the nucleus, and thus likely a correlate of somadendritic size. The exceptional separation of eye position and eye velocity signals into two separate hindbrain nuclei represents an ideal model for understanding the precerebellar projection to the vestibulocerebellum.