bluuebunny/crossref_metadata_2025 huggingface dataset:
Dendritic Cells Are Recruited into the Airway Epithelium during the Inflammatory Response to a Broad Spectrum of Stimuli
Authors: McWilliam Andrew S. , Napoli Sylvia , Marsh Amanda M. , Pemper Francis L. , Nelson Delia J. , Pimm Carolyn L. , Stumbles Philip A. , Wells Timothy N.C. , Holt Patrick G.
Published: June 2004

A key rate-limiting step in the adaptive immune response at peripheral challenge sites is the transmission of antigen signals to T cells in regional lymph nodes. Recent evidence suggests that specialized dendritic cells (DC) fulfill this surveillance function in the resting state, but their relatively slow turnover in most peripheral tissues brings into question their effectiveness in signaling the arrival of highly pathogenic sources of antigen which require immediate mobilization of the full range of host defenses for maintenance of homeostasis. However, the present report demonstrates that recruitment of a wave of DC into the respiratory tract mucosa is a universal feature of the acute cellular response to local challenge with bacterial, viral, and soluble protein antigens. Consistent with this finding, we also demonstrate that freshly isolated respiratory mucosal DC respond in vitro to a variety of CC chemokines as well as complementary cleavage products and N-formyl-methionyl-leucine-phenylalanine. This suggests that rapid amplification of specific antigen surveillance at peripheral challenge sites is an integral feature of the innate immune response at mucosal surfaces, and serves as an “early warning system” to alert the adaptive immune system to incoming pathogens.
Efficient Interaction of HIV-1 with Purified Dendritic Cells via Multiple Chemokine Coreceptors
Authors: Granelli-Piperno Angela , Moser Bernhard , Pope Melissa , Chen Dongling , Wei Yang , Isdell Frank , O'Doherty Una , Paxton William , Koup Richard , Mojsov Svetlana , Bhardwaj Nina , Clark-Lewis Ian , Baggiolini Marco , Steinman Ralph M.
Published: June 2004

HIV-1 actively replicates in dendritic cell (DC)-T cell cocultures, but it has been difficult to demonstrate substantial infection of purified mature DCs. We now find that HIV-1 begins reverse transcription much more efficiently in DCs than T cells, even though T cells have higher levels of CD4 and gp120 binding. DCs isolated from skin or from blood precursors behave similarly. Several M-tropic strains and the T-tropic strain IIIB enter DCs efficiently, as assessed by the progressive formation of the early products of reverse transcription after a 90-min virus pulse at 37°C. However, few late gag-containing sequences are detected, so that active viral replication does not occur. The formation of these early transcripts seems to follow entry of HIV-1, rather than binding of virions that contain viral DNA. Early transcripts are scarce if DCs are exposed to virus on ice for 4 h, or for 90 min at 37°C, conditions which allow virus binding. Also the early transcripts once formed are insensitive to trypsin. The entry of a M-tropic isolates is blocked by the chemokine RANTES, and the entry of IIIB by SDF-1. RANTES interacts with CCR5 and SDF-1 with CXCR4 receptors. Entry of M-tropic but not T-tropic virus is ablated in DCs from individuals who lack a functional CCR5 receptor. DCs express more CCR5 and CXCR4 mRNA than T cells. Therefore, while HIV-1 does not replicate efficiently in mature DCs, viral entry can be active and can be blocked by chemokines that act on known receptors for M- and T-tropic virus.
THE RELATION OF BACTERIOLYSIS TO PROTEOLYSIS
Authors: Jobling James W. , Petersen William
Published: June 2004

1. There is no demonstrable increase in non-coagulable nitrogen during bacteriolysis.

2. Bacteria treated with immune serum and complement are so altered that they are more readily digested by trypsin.

3. Bacteria treated with complement alone become more resistant to proteolysis.

4. Bacteria treated with an excess of immune serum and complement become more resistant to proteolysis.
STUDIES ON THE CHEMISTRY OF SEROUS EFFUSIONS
Authors: Epstein Albert A.
Published: June 2004

A comparison of the results obtained in the analysis of the different effusions shows that they vary, (1) according to location, and (2) according to the disease in which they are produced. Thus the subcutaneous effusions are totally different in their composition from the abdominal or pleuritic fluids; and again the abdominal fluid of nephritic origin is different from those of cardiac or other origin.

The cutaneous effusions are characterized by a very low protein content and a small amount of incoagulable nitrogen. Of the protein present in these fluids, the globulin constitutes the greater portion. In the mixed cardionephritic fluids the ratio of globulin to albumin is lower than that in normal blood serum; but when compared with the blood sera of cardionephritic cases there appears to be a certain parallelism. The chloride content of these fluids is considerably above that found in normal blood serum, but is comparable with those of corresponding cases.

The effusions occurring in serous cavities differ from the cutaneous ones by their higher protein content. The highest values are attained in the pleural fluids, in which the protein present is almost the same as that in normal blood serum. The incoagulable nitrogen in these fluids is uniformly low. The chlorides vary in amount according to the nature of the case. In the effusions of inflammatory origin the values are lower than those found in the blood. In the pleural fluids of other than inflammatory origin the chloride content is either the same or higher than that of blood serum. The globulin-albumin ratio in all of these fluids except one (table III, fluid 61) is higher than that of normal blood serum. Otherwise the highest value is presented by a pleural fluid from a case of nephritis (table III, fluid 205) and the lowest by an empyema fluid (table III, fluid 30). The latter case is of especial interest because of the theory, first propounded by Schmidt, that the leucocytes in the purulent fluid are largely responsible for high globulin content.

The abdominal fluids in general are less rich in protein than the pleural effusions. Those of cardiac origin give the highest protein values, but the globulin-albumin ratios are lower than in the pleural fluids or in the blood sera of corresponding cases. Only in two fluids does the globulin reach a percentage of 62 and 52.2. In both these cases the chloride content is also high. The incoagulable nitrogen in all of them is rather low. In one fluid of purely nephritic origin the protein content is low and all of it is globulin. This is suggestive, when compared with the values obtained in the analysis of the blood sera from nephritic cases. The results obtained in the analysis of abdominal fluids from cardionephritic cases approach very closely those obtained in purely cardiac cases.
ON THE GREATER SUSCEPTIBILITY OF AN ALIEN VARIETY OF HOST TO AN AVIAN TUMOR
Authors: Rous Peyton , Lange Linda B.
Published: June 2004

A transplantable sarcoma of the fowl, known as Chicken Tumor XVIII, in our series, succeeds better in chickens of an alien breed (Plymouth Rock) than in those of the variety in which it originated (brown Leghorn). This is not due to gross physical differences in the two breeds but to some more subtle factor and one which perhaps acts by influencing the agent causing the tumor. It would seem that Chicken Tumor XVIII, as it occurred in nature, was an instance of a disease appearing spontaneously in an animal of relatively insusceptible variety.
LIPOIDS AS INHIBITORS OF ANAPHYLACTIC SHOCK
Authors: Jobling James W. , Petersen William
Published: June 2004

1. The antitryptic titer of the serum can be increased by subcutaneous injections of serum lipoids (antitrypsin) and of the lipoids from egg yolk.

2. Animals so injected show a relative immunity to acute anaphylactic shock (two minimum lethal doses).

3. Extraction of lipoids contained in antigens increases the toxicity of the antigen when injected into a sensitized animal.

4. Sublethal doses of soap solutions injected simultaneously with the antigen (purified horse serum albumen) prevent anaphylactic shock.

5. The refractory state following anaphylactic shock is related in part to an increase in the antitryptic titer of the serum.
FURTHER EXPERIMENTS UPON THE EFFECTS OF EXTIRPATION OF THE THYMUS IN RATS, WITH SPECIAL REFERENCE TO THE ALLEGED PRODUCTION OF RACHITIC LESIONS
Authors: Pappenheimer Alwin M.
Published: June 2004

Rachitic changes in the bones and teeth occur in young albino rats as the result of spontaneous disease, possibly of infective origin. This disease is often, but not always, accompanied by an arrest of growth and malnutrition.

There is no valid reason for attributing such lesions to the loss of thymic function. In some of the rats showing the disease, an unusual number of mitoses were found in the parathyroid glands, but no evidence of injury to these structures.

It has not been found possible to confirm the statements of Klose and Magnini as to the fatal effects of complete thymus extirpation in rats.
DO SUBSTANCES INHIBITING TUMOR GROWTH EXERT A RETARDING INFLUENCE ON THE REGENERATION OF THE SKIN?
Authors: Leighton William E.
Published: June 2004

Repeated injections of colloidal copper, hirudin, nucleoprotein, and casein, which have a definite retarding influence on tumor growth, given to mice during the process of wound healing do not produce any noticeable influence on the course of regeneration.
OBSERVATIONS ON EXPERIMENTAL TYPHOID INFECTION OF THE GALL BLADDER IN THE RABBIT
Authors: Nichols Henry J.
Published: June 2004

1. Besredka's living sensitized vaccine, given intravenously, does not produce a typhoid lesion of the gall bladder in the rabbit.

2. The first transplant of this vaccine is capable of producing this lesion. Hence this vaccine is not entirely safe to handle.

3. Regular infections of the gall bladder have not been produced by carrying a known pathogenic strain on rabbit blood agar, by successive passage through animals, or by the use of freshly isolated strains.

4. No evidence could be demonstrated in the rabbit of the immunity produced in man by vaccination with a whole killed vaccine.

5. Vaccine treatment did not cure the gall bladder lesion.

6. With the present methods of producing infections in the chimpanzee and the rabbit, neither of these animals is suitable for deciding the problems of the immunization of man by vaccines. These problems must be settled, as some of them already have been settled, by actual experience with large numbers of men kept under close observation.
THE INHIBITION OF THE TOXICITY OF URANIUM NITRATE BY SODIUM CARBONATE, AND THE PROTECTION OF THE KIDNEY ACUTELY NEPHROPATHIC FROM URANIUM FROM THE TOXIC ACTION OF AN ANESTHETIC BY SODIUM CARBONATE
Authors: MacNider William Deb.
Published: June 2004

1. The toxicity of uranium in animals of different ages is associated with the power of the metal to lead to the formation of organic acids, as, for instance, diacetic acid and also acetone.

2. The power of sodium carbonate to lessen the toxicity of uranium depends upon its power to delay the formation of such bodies and to cause their appearance in the urine in lessened amounts, and does not depend upon the power of the carbonate to detoxicate the metal.

3. The protection of the kidney by the carbonate, which is shown by the kidney being functionally much more active during an anesthesia than the kidney of a control animal, and by the Jack of fatty degeneration, acute swelling, and necrosis of the renal epithelium which is constantly seen in the unprotected kidneys, is probably dependent upon two factors: the neutralization of organic acids formed prior to and during the anesthesia, and the neutralization of hydrochloric acid which Graham has shown to be liberated by chloroform during an anesthesia induced by this substance.
INTRATESTICULAR IMPLANTATION OF THE FLEXNER-JOBLING RAT CARCINOMA
Authors: Woglom William H.
Published: June 2004

The Flexner-Jobling adenocarcinoma of the rat is easily transplantable into the testis of this animal.

The resulting growths in the intact testis do not often attain the size of subcutaneous tumors.

The smaller size of intratesticular nodules can not be explained solely by the pressure to which they are subjected during their growth; other factors, which cannot be determined, appear to be concerned.
EXPERIMENTAL SYPHILIS IN THE RABBIT PRODUCED BY THE BRAIN SUBSTANCE OF THE LIVING PARETIC
Authors: Wile Udo J.
Published: June 2004

1. Spirochætes from the living paretic brain easily infect rabbits with experimental syphilis.

2. They constitute a virulent strain with a shorter period of incubation for the rabbit than exists with other strains.
THE BACTERICIDAL PROPERTIES OF THE QUATERNARY SALTS OF HEXAMETHYLENETETRAMINE
Authors: Jacobs Walter A. , Heidelberger Michael , Bull Carroll G.
Published: June 2004

The extension of the study of the quaternary salts of hexamethylenetetramine to those obtained by the addition of this base to the most varied types of substances containing aliphatically bound halogen has demonstrated that the introduction of the hexamethylenetetramine nucleus in this manner results in the production of bactericidal substances or enhances the bactericidal action if already present.

In particular it was found possible by the use of the halogenacetyl group, XCH2CO, as a connecting link, to furnish primary and secondary aliphatic and aromatic amines, alcohols, and hydrocarbons of the most varied character with the hexamethylenetetramine molecule and to study the relation between chemical constitution and bactericidal action in the series of substances so prepared. Because of the variety of chemical types studied, the results are too involved for a detailed summary here.

Many of the substances were found to be very powerful bactericides, and in a number of instances derivatives of purely aliphatic nature were found to possess an unusual bactericidal power.

Bacillus typhosus, streptococcus, meningococcus, and gonococcus were the microorganisms used for the tests, and striking instances of partial specificity were observed. This specificity was found to favor not one species alone, but instances were found in which each of the types of bacilli was shown to be especially susceptible to one or another of the particular types of compound employed. The source of this partial specificity is to be sought not in the hexamethylenetetramine nucleus itself but in the molecule to which it is attached.

The action of some of the substances was tested in the presence of serum or protein and was found to be not at all or only slightly inhibited. In other cases marked inhibition occurred. The factors controlling the serum- or protein-compatibility of these substances are likewise to be sought in that portion of the molecule other than the hexamethylenetetramine.
THE PROTECTION OF PATHOGENIC MICROORGANISMS BY LIVING TISSUE CELLS
Authors: Rous Peyton , Jones F. S.
Published: June 2004

1. Living phagocytes are able to protect ingested organisms from the action of destructive substances in the surrounding fluid, and even from a strong homologous antiserum.

2. There is evidence that the protection by phagocytes is largely if not entirely conditioned on their being alive.

3. These facts should be taken into consideration in the study of diseases caused by infectious agents capable of living within tissue cells.
Trust among Strangers
Authors: Bicchieri Cristina , Duffy John , Tolle† Gil
Published: June 2004

The paper presents a simulation of the dynamics of impersonal trust. It shows how a “trust and reciprocate” norm can emerge and stabilize in populations of conditional cooperators. The norm, or behavioral regularity, is not to be identified with a single strategy. It is instead supported by several conditional strategies that vary in the frequency and intensity of sanctions.
A Type V Myosin (Myo2p) and a Rab-like G-Protein (Ypt11p) Are Required for Retention of Newly Inherited Mitochondria in Yeast Cells during Cell Division
Authors: Boldogh Istvan R. , Ramcharan Sharmilee L. , Yang Hyeong-Cheol , Pon Liza A.
Published: June 2004

Two actin-dependent force generators contribute to mitochondrial inheritance: Arp2/3 complex and the myosin V Myo2p (together with its Rab-like binding partner Ypt11p). We found that deletion of YPT11, reduction of the length of the Myo2p lever arm (myo2-Δ6IQ), or deletion of MYO4 (the other yeast myosin V), had no effect on mitochondrial morphology, colocalization of mitochondria with actin cables, or the velocity of bud-directed mitochondrial movement. In contrast, retention of mitochondria in the bud was compromised in YPT11 and MYO2 mutants. Retention of mitochondria in the bud tip of wild-type cells results in a 60% decrease in mitochondrial movement in buds compared with mother cells. In ypt11Δ mutants, however, the level of mitochondrial motility in buds was similar to that observed in mother cells. Moreover, the myo2-66 mutant, which carries a temperature-sensitive mutation in the Myo2p motor domain, exhibited a 55% decrease in accumulation of mitochondria in the bud tip, and an increase in accumulation of mitochondria at the retention site in the mother cell after shift to restrictive temperatures. Finally, destabilization of actin cables and the resulting delocalization of Myo2p from the bud tip had no significant effect on the accumulation of mitochondria in the bud tip.
Transcriptional Response of Yeast to Aflatoxin B1: Recombinational Repair InvolvingRAD51andRAD1
Authors: Keller-Seitz Monika U. , Certa Ulrich , Sengstag Christian , Würgler Friedrich E. , Sun Mingzeng , Fasullo Michael
Published: June 2004

The potent carcinogen aflatoxin B1is a weak mutagen but a strong recombinagen in Saccharomyces cerevisiae. Aflatoxin B1exposure greatly increases frequencies of both heteroallelic recombination and chromosomal translocations. We analyzed the gene expression pattern of diploid cells exposed to aflatoxin B1using high-density oligonucleotide arrays comprising specific probes for all 6218 open reading frames. Among 183 responsive genes, 46 are involved in either DNA repair or in control of cell growth and division. Inducible growth control genes include those in the TOR signaling pathway and SPO12, whereas PKC1 is downregulated. Eleven of the 15 inducible DNA repair genes, including RAD51, participate in recombination. Survival and translocation frequencies are reduced in the rad51 diploid after aflatoxin B1exposure. In mec1 checkpoint mutants, aflatoxin B1exposure does not induce RAD51 expression or increase translocation frequencies; however, when RAD51 is constitutively overexpressed in the mec1 mutant, aflatoxin B1exposure increased translocation frequencies. Thus the transcriptional profile after aflatoxin B1exposure may elucidate the genotoxic properties of aflatoxin B1.
A comparative method for identification of gene structures and alternatively spliced variants
Authors: Chuang Trees-Juen , Chen Feng-Chi , Chou Meng-Yuan
Published: June 2004

Motivation: Alternative splicing (AS) serves as a mechanism to create diversity among functional proteins. Increasing evidence indicates that a large portion of genes have AS forms. Hence AS variants should be considered while analyzing gene structures.

Results: A new cross-species gene identification and AS analysis system, PSEP, has been developed. The system is based on expressed sequence tag (EST)-to-genome and genome-to-genome comparisons and is implemented in two steps: sequence alignment and a series of post-alignment processes, including progressive signal extraction and patching. For gene identification, these post-alignment processes serve as noise filters and enable PSEP to eliminate ∼88% of potential overprediction. The overall accuracy of PSEP is better than or comparable to that of other well-known cross-species gene prediction programs, including the ROSETTA program, TWINSCAN, SGP-1/-2 and SLAM, when tested on three benchmark datasets (the ELN gene region, the HoxA cluster and the ROSETTA set). In addition, 76.2 and 76.0% of multiple-exon genes in the ROSETTA dataset and human chromosome 20, respectively, are found to have AS forms. Approximately 23% of the 210 elementary alternatives identified in the ROSETTA dataset are not conserved between the human and mouse genomes, and none of the 210 transcripts is found in the RefSeq annotation. With its dual functions in cross-species conserved sequence analysis and AS analysis, PSEP is highly suitable for studying the evolution of AS patterns and for finding unidentified gene expression features.

Availability: The programs of PESP as well as the visualization tool required to build the proposed annotation scheme are available at ttp://www.sinica.edu.tw/~trees/PSEP/.
Developing optimal non-linear scoring function for protein design
Authors: Hu Changyu , Li Xiang , Liang Jie
Published: June 2004

Motivation. Protein design aims to identify sequences compatible with a given protein fold but incompatible to any alternative folds. To select the correct sequences and to guide the search process, a design scoring function is critically important. Such a scoring function should be able to characterize the global fitness landscape of many proteins simultaneously.

Results: To find optimal design scoring functions, we introduce two geometric views and propose a formulation using a mixture of non-linear Gaussian kernel functions. We aim to solve a simplified protein sequence design problem. Our goal is to distinguish each native sequence for a major portion of representative protein structures from a large number of alternative decoy sequences, each a fragment from proteins of different folds. Our scoring function discriminates perfectly a set of 440 native proteins from 14 million sequence decoys. We show that no linear scoring function can succeed in this task. In a blind test of unrelated proteins, our scoring function misclassfies only 13 native proteins out of 194. This compares favorably with about three–four times more misclassifications when optimal linear functions reported in the literature are used. We also discuss how to develop protein folding scoring function.

Availability: Available on request from the authors.
Comparison of probabilistic combination methods for protein secondary structure prediction
Authors: Liu Yan , Carbonell Jaime , Klein-Seetharaman Judith , Gopalakrishnan Vanathi
Published: June 2004

Motivation: Protein secondary structure prediction is an important step towards understanding how proteins fold in three dimensions. Recent analysis by information theory indicates that the correlation between neighboring secondary structures are much stronger than that of neighboring amino acids. In this article, we focus on the combination problem for sequences, i.e. combining the scores or assignments from single or multiple prediction systems under the constraint of a whole sequence, as a target for improvement in protein secondary structure prediction.

Results: We apply several graphical chain models to solve the combination problem and show that they are consistently more effective than the traditional window-based methods. In particular, conditional random fields (CRFs) moderately improve the predictions for helices and, more importantly, for beta sheets, which are the major bottleneck for protein secondary structure prediction.
Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes
Authors: Hsiao A. , Worrall D. S. , Olefsky J. M. , Subramaniam S.
Published: June 2004

Motivation: Microarrays are becoming an increasingly common tool for observing changes in gene expression over a large cross section of the genome. This experimental tool is particularly valuable for understanding the genome-wide changes in gene transcription in response to thiazolidinedione (TZD) treatment. The TZD class of drugs is known to improve insulin-sensitivity in diabetic patients, and is clinically used in treatment regimens. In cells, TZDs bind to and activate the transcriptional activity of peroxisome proliferator-activated receptor gamma (PPAR-γ). Large-scale array analyses will provide some insight into the mechanisms of TZD-mediated insulin sensitization. Unfortunately, a theoretical basis for analyzing array data has not kept pace with the rapid adoption of this tool. The methods that are commonly used, particularly the fold-change approach and the standard t-test, either lack statistical rigor or resort to generalized statistical models that do not accurately estimate variability at low replicate numbers.

Results: We introduce a statistical framework that models the dependence of measurement variance on the level of gene expression in the context of a Bayesian hierarchical model. We compare several methods of parameter estimation and subsequently apply these to determine a set of genes in 3T3-L1 adipocytes that are differentially regulated in response to TZD treatment. When the number of experimental replicates is low (n = 2–3), this approach appears to qualitatively preserve an equivalent degree of specificity, while vastly improving sensitivity over other comparable methods. In addition, the statistical framework developed here can be readily applied to understand the implicit assumptions made in traditional fold-change approaches to array analysis.

Availability: Our statistical approach is implemented as a set of Java-based tools called VAMPIRE, accessible from our website at http://genome.ucsd.edu/VAMPIRE
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences
Authors: Bonnet Eric , Wuyts Jan , Rouzé Pierre , Van de Peer Yves
Published: June 2004

Motivation: Most non-coding RNAs are characterized by a specific secondary and tertiary structure that determines their function. Here, we investigate the folding energy of the secondary structure of non-coding RNA sequences, such as microRNA precursors, transfer RNAs and ribosomal RNAs in several eukaryotic taxa. Statistical biases are assessed by a randomization test, in which the predicted minimum free energy of folding is compared with values obtained for structures inferred from randomly shuffling the original sequences.

Results: In contrast with transfer RNAs and ribosomal RNAs, the majority of the microRNA sequences clearly exhibit a folding free energy that is considerably lower than that for shuffled sequences, indicating a high tendency in the sequence towards a stable secondary structure. A possible usage of this statistical test in the framework of the detection of genuine miRNA sequences is discussed.

Availability: The dataset, software and additional data files are freely available as supplementary information on our Website.

Supplementary information:  http://www.psb.ugent.be/bioinformatics/
A web portal for classification of expression data using maximal margin linear programming
Authors: Antonov Alexey V. , Tetko Igor V. , Prokopenko Volodymyr V. , Kosykh Denis , Mewes Hans W.
Published: June 2004

Summary: The Maximal Margin (MAMA) linear programming classification algorithm has recently been proposed and tested for cancer classification based on expression data. It demonstrated sound performance on publicly available expression datasets. We developed a web interface to allow potential users easy access to the MAMA classification tool. Basic and advanced options provide flexibility in exploitation. The input data format is the same as that used in most publicly available datasets. This makes the web resource particularly convenient for non-expert machine learning users working in the field of expression data analysis.

Availability: The web software developed is available at http://mips.gsf.de/proj/mdcs/. A stand-alone version of the server can be downloaded from this site too.
Phan3D: design of biological phantoms in 3D electron microscopy
Authors: Bilbao-Castro J. R. , Sorzano C. O. S. , García I. , Fernández J. J.
Published: June 2004

Summary: Three-Dimensional Electron Microscopy (3DEM) has turned out to be a major player in structural proteomics. In 3DEM, tens of thousands of EM images from a macromolecule at different views are combined to derive its structure by means of a 3D reconstruction algorithm. However, for an optimal reconstruction, the most suitable algorithm has to be used and its parameters have to be tuned for the macromolecule under study and the experimental conditions found. The use of phantoms is central to objective comparison of reconstruction algorithms and optimization of their parameters. Phan3D is a tool intended to provide a fully visual and interactive environment that facilitates the design of phantoms resembling biological specimens in 3DEM. Phan3D has been developed as an alternative to the tedious, error-prone and old-fashioned phantom design that is based on hand-written text description files.

Availability: Phan3D has been integrated into Xmipp: http://biocomp.cnb.uam.es/Biocomp/public/Software/
The UniMarker (UM) method for synteny mapping of large genomes
Authors: Liao Ben-Yang , Chang Yu-Jung , Ho Jan-Ming , Hwang Ming-Jing
Published: June 2004

Motivation: Synteny mapping, or detecting regions that are orthologous between two genomes, is a key step in studies of comparative genomics. For completely sequenced genomes, this is increasingly accomplished by whole-genome sequence alignment. However, such methods are computationally expensive, especially for large genomes, and require rather complicated post-processing procedures to filter out non-orthologous sequence matches.

Results: We have developed a novel method that does not require sequence alignment for synteny mapping of two large genomes, such as the human and mouse. In this method, the occurrence spectra of genome-wide unique 16mer sequences present in both the human and mouse genome are used to directly detect orthologous genomic segments. Being sequence alignment-free, the method is very fast and able to map the two mammalian genomes in one day of computing time on a single Pentium IV personal computer. The resulting human–mouse synteny map was shown to be in excellent agreement with those produced by the Mouse Genome Sequencing Consortium (MGSC) and by the Ensembl team; furthermore, the syntenic relationship of segments found only by our method was supported by BLASTZ sequence alignment.

Availability: The source code of our method and the resulting human–mouse synteny maps have been placed at http://synteny.ibms.sinica.edu.tw/ for free access.

Supplementary information: Seven supplementary figures can be found at the same website.
Quantitative Leverage Through Qualitative Knowledge: Augmenting the Statistical Analysis of Complex Causes
Authors: Gordon Sanford C. , Smith Alastair
Published: June 2004

Social scientific theories frequently posit that multiple causal mechanisms may produce the same outcome. Unfortunately, it is not always possible to observe which mechanism was responsible. For example, IMF scholars conjecture that nations enter IMF agreements both out of economic need and for discretionary domestic political reasons. Typically, though, all we observe is the fact of agreement, not its cause. Partial observability probit models (Poirier 1980,Journal of Econometrics12:209–217; Braumoeller 2003,Political Analysis11:209–233) provide one method for the statistical analysis of such phenomena. Unfortunately, they are often plagued by identification and labeling difficulties. Sometimes, however, qualitative studies of particular cases enlighten us about causes when quantitative studies cannot. We propose exploiting this information to lend additional structure to the partial observability approach. Monte Carlo simulation reveals that by anchoring “discernible” causes for a handful of cases about which we possess qualitative information, we obtain greater efficiency. More important, our method proves reliable at recovering unbiased parameter estimates when the partial observability model fails. The paper concludes with an analysis of the determinants of IMF agreements.

A member shall be entitled to purchase the currencies of other members from the Fund …[provided] the member represents that it has a need to make the purchase because of its balance of payments or its reserve position or developments in its reserves.

—International Monetary Fund Articles of Agreement

[IMF] negotiations sometimes enable government leaders to do what they privately wish to do, but are powerless to do domestically.

—Robert Putnam (1988, p. 457)
Presidential Elections and the Stock Market: Comparing Markov-Switching and Fractionally Integrated GARCH Models of Volatility
Authors: Leblang David , Mukherjee Bumba
Published: June 2004

Existing research on electoral politics and financial markets predicts that when investors expect left parties—Democrats (US), Labor (UK)—to win elections, market volatility increases. In addition, current econometric research on stock market volatility suggests that Markov-switching models provide more accurate volatility forecasts and fit stock price volatility data better than linear or nonlinear GARCH (generalized autoregressive conditional heteroskedasticity) models. Contrary to the existing literature, we argue here that when traders anticipate that the Democratic candidate will win the presidential election, stock market volatility decreases. Using two data sets from the 2000 U.S. presidential election, we test our claim by estimating several GARCH, exponential GARCH (EGARCH), fractionally integrated exponential GARCH (FIEGARCH), and Markov-switching models. We also conduct extensive forecasting tests—including RMSE and MAE statistics as well as realized volatility regressions—to evaluate these competing statistical models. Results from forecasting tests show, in contrast to prevailing claims, that GARCH and EGARCH models provide substantially more accurate forecasts than the Markov-switching models. Estimates from all the statistical models support our key prediction that stock market volatility decreases when traders anticipate a Democratic victory.
IL8 release, tight junction and cytoskeleton dynamic reorganization conducive to permeability increase are induced by dengue virus infection of microvascular endothelial monolayers
Authors: Talavera Dodanim , Castillo Aida M. , Dominguez M. C. , Gutierrez Alejandro Escobar , Meza Isaura
Published: June 2004

Permeability alterations of microvascular endothelia may be a factor in the plasma leakage produced by dengue virus infection. Confluent monolayers of the human dermal microvascular endothelial cell line HMEC-1 were utilized as an experimental model to study the cellular responses induced by the virus. Infected monolayers showed increased permeability for [3H]mannitol, but no changes were observed for 4–70 kDa dextrans at 48 h post-infection (p.i.), a time at which viral titres reached maximal values and 40 % of the cells expressed viral proteins. A further increase in permeability occurred at 72 h, still without evident cytopathic effects on the monolayer. Coinciding with this, actin was reorganized in the infected cells and the tight junction protein occludin was displaced to the cytoplasm. Increments in the thickness of stress fibres and focal adhesions were observed in uninfected cells neighbouring infected cells. Culture medium from infected monolayers induced permeability changes and thickening of actin-containing structures in control cultures that resembled those observed 48 h p.i. Interleukin (IL) 8 was found in culture medium at concentrations ranging from 20 to 100 pg ml−1. Neutralizing antibodies against IL8 partially inhibited the changes produced by the culture medium as well as those induced by addition of IL8. Genistein inhibited the effect of the culture medium and the phosphorylation of proteins associated with focal adhesions and indicated the participation of tyrosine kinases. These findings suggest that IL8 production by infected monolayers contributes to the virus-induced effect on the cytoskeleton and tight junctions and thereby modifies transendothelial permeability.
Amino acid changes in functional domains of latent membrane protein 1 of Epstein–Barr virus in nasopharyngeal carcinoma of southern China and Taiwan: prevalence of an HLA A2-restricted ‘epitope-loss variant’
Authors: Lin Jung-Chung , Cherng Jaw-Ming , Lin Hsiung-Ju , Tsang Chi-Wai , Liu Yi-Xi , Lee Steven P.
Published: June 2004

Full-length sequences of the Epstein–Barr virus (EBV) gene for latent membrane protein (LMP)-1 from 22 nasopharyngeal carcinoma (NPC) biopsy specimens and 18 non-neoplastic counterparts (NPI) were determined. Relative to the B95-8 strain, the amino acid sequences of the toxic-signal and transformation domains were changed variably in NPC and NPI specimens; in contrast, no change was observed in the NF-κB (nuclear factorκB) activation domain. HLA typing revealed that 47 % of NPC and 31 % of NPI specimens were HLA A2-positive. A major A2-restricted epitope within LMP-1 (residues 125–133) was analysed. At residue 126, a change of L→F was detected in 91 % (20/22) of NPC and 67 % (12/18) of NPI specimens. In addition, a deletion at residue 126 was detected in one NPC sample from Taiwan. At residue 129, a change of M→I was observed in all samples, regardless of whether they were NPC or NPI. The changes in this peptide between NPC and NPI specimens, including mutation and deletion, are statistically significant (P<0·05). A recent report indicated that this variant sequence is recognized poorly by epitope-specific T cells. Genotyping results indicated that 96 % of NPC and 67 % of NPI samples carried a type A virus. By scanning the entire sequence of LMP-1, eight distinct patterns were identified. Detailed examination of these patterns revealed that type A strains are more prevalent in NPC than in NPI specimens and are marked by the loss of anXhoI site, the presence of a 30 bp deletion and the presence of a mutated, A2-restricted, T cell target epitope sequence. These results suggest that an EBV strain carrying an HLA A2-restricted ‘epitope-loss variant’ of LMP-1 is prevalent in NPC in southern China and Taiwan.
Sialidase, receptor-binding and fusion-promotion activities of Newcastle disease virus haemagglutinin–neuraminidase glycoprotein: a mutational and kinetic study
Authors: Ferreira Laura , Muñoz-Barroso Isabel , Marcos Fernando , Shnyrov Valery L. , Villar Enrique
Published: June 2004

Mutations were generated in residues at the putative catalytic site of the haemagglutinin–neuraminidase (HN) protein of Newcastle disease virus Clone 30 strain (Arg498, Glu258, Tyr262, Tyr317 and Ser418) and their effects on its three associated activities were studied. Expression of the mutant proteins at the surface of HeLa cells was similar to that of the wild-type. Sialidase, receptor-binding and fusion-promotion activities were affected to different degrees for all mutants studied. Mutant Arg498Lys lost most of its sialidase activity, although it retained most of the receptor-binding activity, suggesting that, for the former activity, besides the presence of a basic residue, the proximity to the substrate molecule is also important, as Lys is shorter than Arg. Proximity also seems to be important in substrate recognition, since Tyr262Phe retained most of its sialidase activity while Tyr262Ser lost most of it. Also, Ser418Ala displayed most of the wild-type sialidase activity. However, a kinetic and thermodynamic study of the sialidase activity of the Tyr262Ser and Ser418Ala mutants was performed and revealed that the hydroxyl group of these residues also plays an important role in catalysis, since such activity was much less effective than that of the wild-type and these mutations modified their activation energy for sialidase catalysis. The discrepancy of the modifications in sialidase and receptor-binding activities in the mutants analysed does not account for the topological coincidence of the two sites. These results also suggest that the globular head of HN protein may play a role in fusion-promotion activity.
Evolution of naturally occurring 5′ non-translated region variants of hepatitis C virus genotype 1b in selectable replicons
Authors: van Leeuwen Hans C. , Reusken Chantal B. E. M. , Roeten Marko , Dalebout Tim J. , Riezu-Boj Jose Ignacio , Ruiz Juan , Spaan Willy J. M.
Published: June 2004

Quasispecies shifts are essential for the development of persistent hepatitis C virus (HCV) infection. Naturally occurring sequence variations in the 5′ non-translated region (NTR) of the virus could lead to changes in protein expression levels, reflecting selective forces on the virus. The extreme 5′ end of the virus' genome, containing signals essential for replication, is followed by an internal ribosomal entry site (IRES) essential for protein translation as well as replication. The 5′ NTR is highly conserved and has a complex RNA secondary structure consisting of several stem–loops. This report analyses the quasispecies distribution of the 5′ NTR of an HCV genotype 1b clinical isolate and found a number of sequences differing from the consensus sequence. The consensus sequence, as well as a major variant located in stem–loop IIIa of the IRES, was investigated using self-replicating HCV RNA molecules in human hepatoma cells. The stem–loop IIIa mutation, which is predicted to disrupt the stem structure, showed slightly lower translation efficiency but was severely impaired in the colony formation of selectable HCV replicons. Interestingly, during selection of colonies supporting autonomous replication, mutations emerged that restored the base pairing in the stem–loop. Recloning of these altered IRESs confirmed that these second site revertants were more efficient in colony formation. In conclusion, naturally occurring variants in the HCV 5′ NTR can lead to changes in their replication ability. Furthermore, IRES quasispecies evolution was observed in vitro under the selective pressure of the replicon system.
Structure of pre-S2 N- and O-linked glycans in surface proteins from different genotypes of hepatitis B virus
Authors: Schmitt Sigrid , Glebe Dieter , Tolle Tanja K. , Lochnit Günter , Linder Dietmar , Geyer Rudolf , Gerlich Wolfram H.
Published: June 2004

The middle-sized (M) surface proteins of hepatitis B virus (HBV) and other orthohepadnaviruses contain a conservedN-glycan in their pre-S2 domain, which is essential for the secretion of viral particles. Recently, we also foundO-glycans in the pre-S2 domain of M protein from woodchuck hepatitis virus (WHV) and HBV genotype D. Since theO-glycosylation motif is not conserved in all genotypes of HBV, the glycosylation patterns of HBV genotypes A and C were analysed. Pre-S2 (glyco)peptides were released from HBV-carrier-derived HBV subviral particles by tryptic digestion, purified by reversed-phase HPLC and identified by amino acid and amino-terminal sequence analysis as well as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Pre-S2N-glycans were characterized by anion-exchange chromatography, methylation analysis and on-target sequential exoglycosidase digestions in combination with MALDI-TOF-MS, demonstrating the presence of partially sialylated diantennary complex-type oligosaccharides in all genotypes examined. Pre-S2O-glycans were characterized by on-target sequential exoglycosidase digestions in combination with MALDI-TOF-MS. The pre-S2 domain of M protein and, to a minor extent, of L (large) protein from HBV genotype C and D was partiallyO-glycosylated by Neu5Ac(α2–3)Gal(β1–3)GalNAcα- or Gal(β1–3)GalNAcα-units at Thr-37 within a conserved sequence context. Genotype A, containing no Thr at position 37 or 38, was notO-glycosylated. Analytical data further revealed that M protein is mostly amino-terminally acetylated in all examined genotypes and that the terminal methionine is partially oxidized. The findings may be relevant for the secretion and the immunogenicity of HBV.
Identification of an amino acid residue on influenza C virus M1 protein responsible for formation of the cord-like structures of the virus
Authors: Muraki Yasushi , Washioka Hiroshi , Sugawara Kanetsu , Matsuzaki Yoko , Takashita Emi , Hongo Seiji
Published: June 2004

Influenza C virus-like particles (VLPs) have been generated from cloned cDNAs. A cDNA of the green fluorescent protein (GFP) gene in antisense orientation was flanked by the 5′ and 3′ non-coding regions of RNA segment 5 of the influenza C virus. The cDNA cassette was inserted between an RNA polymerase I promoter and terminator of the Pol I vector. This plasmid DNA was transfected into 293T cells together with plasmids encoding virus proteins of C/Ann Arbor/1/50 or C/Yamagata/1/88. Transfer of the supernatants of the transfected 293T cells to HMV-II cells resulted in GFP expression in the HMV-II cells. The quantification of the GFP-positive HMV-II cells indicated the presence of approximately 106 VLPs (ml supernatant)−1. Cords 50−300 μm in length were observed on transfected 293T cells, although the cords were not observed when the plasmid for M1 protein of C/Ann Arbor/1/50 was replaced with that of C/Taylor/1233/47. A series of transfection experiments with plasmids encoding M1 mutants of C/Ann Arbor/1/50 or C/Taylor/1233/47 showed that an amino acid at residue 24 of the M1 protein is responsible for cord formation. This finding provides direct evidence for a previous hypothesis that M1 protein is involved in the formation of cord-like structures protruding from the C/Yamagata/1/88-infected cells. Evidence was obtained by electron microscopy that transfected cells bearing cords produced filamentous VLPs, suggesting the potential role of the M1 protein in determining the filamentous/spherical morphology of influenza C virus.
Dominant negative effect of wild-type NS5A on NS5A-adapted subgenomic hepatitis C virus RNA replicon
Authors: Graziani Rita , Paonessa Giacomo
Published: June 2004

An efficient model is currently used to study hepatitis C virus (HCV) replication in cell culture. It involves transfection in Huh7, a hepatoma-derived cell line, of an antibiotic (neomycin) selectable HCV subgenomic replicon encoding the non-structural (NS) proteins from NS3 to NS5B. However, strong and sustained replication is achieved only on the appearance of adaptive mutations in viral proteins. The most effective of these adaptive mutations are concentrated mainly in NS5A, not only into the original Con1 but also in the recently established HCV-BK and HCV-H77 isolate-derived replicons. This suggests that the expression of wild-type (wt) NS5A may not allow efficient HCV RNA replication in cell culture. With the use of a β-lactamase reporter gene as a marker for HCV replication and TaqMan RNA analysis, the replication of different HCV replicons in cotransfection experiments was investigated. Comparing wt with NS5A-adapted replicons, the strong evidence accumulated showed that the expression of wt NS5A was actually able to inhibit the replication of NS5A-adapted replicons. This feature was characterized as a dominant negative effect. Interestingly, an NS5B (R2884G)-adapted replicon, containing a wt NS5A, was dominant negative on an NS5A-adapted replicon but was not inhibited by the original Con1 replicon. In conclusion, these studies revealed that the original wt Con1 replicon is not only incompetent for replication in cell culture, but is also able to interfere with NS5A-adapted replicons.