bluuebunny/crossref_metadata_2025_split huggingface dataset:
The small-world dynamics of tree networks
and data mining in phyloinformatics
Authors: Piel William H. , Sanderson Michael J. , Donoghue Michael J. 
Published: June 2003

Abstract
Motivation: A noble and ultimate objective of phyloinformatic research is to assemble, synthesize, and explore the evolutionary history of life on earth. Data mining methods for performing these tasks are not yet well developed, but one avenue of research suggests that network connectivity dynamics will play an important role in future methods. Analysis of disordered networks, such as small-world networks, has applications as diverse as disease propagation, collaborative networks, and power grids. Here we apply similar analyses to networks of phylogenetic trees in order to understand how synthetic information can emerge from a database of phylogenies
Results: Analyses of tree network connectivity in TreeBASE show that a collection of phylogenetic trees behaves as a small-world network—while on the one hand the trees are clustered, like a non-random lattice, on the other hand they have short characteristic path lengths, like a random graph. Tree connectivities follow a dual-scale power-law distribution (first power-law exponent ≈1.87; second ≈4.82). This unusual pattern is due, in part, to the presence of alternative tree topologies that enter the database with each published study. As expected, small collections of trees decrease connectivity as new trees are added, while large collections of trees increase connectivity. However, the inflection point is surprisingly low: after about 600 trees the network suddenly jumps to a higher level of coherence. More stringent definitions of ‘neighbour’ greatly delay the threshold whence a database achieves sufficient maturity for a coherent network to emerge. However, more stringent definitions of ‘neighbour’ would also likely show improved focus in data mining
Availability: http://treebase.org
Contact: wpiel@buffalo.edu
* To whom correspondence should be addressed.
† Current address: Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
Genescript: DNA sequence annotation pipeline
Authors: Hudek Alexander K. , Cheung Joseph , Boright Andrew P. , Scherer Stephen W. 
Published: June 2003

Abstract
Summary: Genescript uses a number of publicly available analysis programs to annotate a DNA sequence. It provides an integrated display of results from each program, and includes an evidence-based scoring system that gives informative summaries of predicted gene models
Availability: Genescript is available for download from http:://tcag.bioinfo.sickkids.on.ca/genescript/
Contact: alex@genet.sickkids.on.ca
* To whom correspondence should be addressed.
Coupled two-way clustering server
Authors: Getz Gad , Domany Eytan 
Published: June 2003

Abstract
Summary: The CTWC server provides access to the software, CTWC1.00, that implements Coupled Two Way Clustering (Getz et al., 2000), a method designed to mine gene expression data
Availability: Free, at http://ctwc.weizmann.ac.il
Contact: ctwc_support@weizmann.ac.il
Supplementary information: The site has a link to an example which provides figures and detailed explanations
* To whom correspondence should be addressed.
Spirituality and Its Discontents: Practices in Jonathan Edwards's Charity and Its Fruits
Authors: Spohn William C. 
Published: June 2003

The contemporary interest in spiritual experience has some theological and ethical ambiguity. To what extent does it reflect genuine engagement with the sacred, to what extent is it dabbling in experience without adequate interpretation or moral commitment? Jonathan Edwards faced similar challenges in his sermons on 1 Cor 13, Charity and Its Fruits. Alasdair MacIntyre and Pierre Hadot have explored the constitutive role of practices in forming of virtues and transmitting a way of life. Their writings help show the continuing relevance of the spiritual practices that Edwards advocated, particularly self‐examination, healing by contraries, and solidarity.
Book Reviews
Authors: RIDOUT M. S. 
Published: June 2003

Visualizing Statistical Models and Concepts(R. W. Farebrother)    C. B. BorkowfStatistical Consulting(J. Cabrera and A. McDougall)    A. CowlingData Monitoring Committees in Clinical Trials: A Practical Perspective(S. S. Ellenberg, T. R. Fleming, and D. L. DeMets)    B. FreidlinCombined Survey Sampling Inference: Weighing Basu's Elephants(K. Brewer)    Y. G. BergerVisualising Categorical Data(M. Friendly)    R. J. MarshallEstimating Animal Abundance: Closed Populations(D. L. Borchers, S. T. Buckland, and W. Zucchini)    A. ChaoLikelihood, Bayesian, and MCMC Methods in Quantitative Genetics(D. Sorensen and D. Gianola)    J. WhittakerBlock Designs: A Randomization Approach, Volumes I and II(T. Caliński and S. Kageyama)    G. M. ClarkeComputational Statistics Handbook with Matlab(W. L. Martinez and A. R. Martinez)    P. K. DunnSpatial Cluster Modelling(A. B. Lawson and D. G. T. Denison, eds.)    D. AllardElements of Computational Statistics(J. E. Gentle)    D. M. SmithBrief Reports by the EditorA First Course in Linear Model Theory(N. Ravishanker and D. K. Dey)Statistical Inference, 2nd edition(P. H. Garthwaite, I. T. Jolliffe, and B. Jones)Statistical Analysis of Designed Experiments, 2nd edition(H. Toutenburg)Logistic Regression: A Self‐Learning Text, 2nd edition(D. G. Kleinbaum and M. Klein)American Series in Mathematical and Management Sciences, Volume 47. USA‐II, Forum for Interdisciplinary Mathematics Proceedings on Statistics, Combinatorics, and Related Areas, Volume II of Proceedings of the University of South Alabama (U.S.A.) Conference (Mobile, Alabama, U.S.A., December 1999)(S. N. Mishra, ed.)
A Live Attenuated Equine Infectious Anemia Virus Proviral Vaccine with a Modified
S2
Gene Provides Protection from Detectable Infection by Intravenous Virulent Virus Challenge of Experimentally Inoculated Horses
Authors: Li Feng , Craigo Jodi K. , Howe Laryssa , Steckbeck Jonathan D. , Cook Sheila , Issel Charles , Montelaro Ronald C. 
Published: June 2003

ABSTRACT

Previous evaluations of inactivated whole-virus and envelope subunit vaccines to equine infectious anemia virus (EIAV) have revealed a broad spectrum of efficacy ranging from highly type-specific protection to severe enhancement of viral replication and disease in experimentally immunized equids. Among experimental animal lentivirus vaccines, immunizations with live attenuated viral strains have proven most effective, but the vaccine efficacy has been shown to be highly dependent on the nature and severity of the vaccine virus attenuation. We describe here for the first time the characterization of an experimental attenuated proviral vaccine, EIAV
UK
ΔS2, based on inactivation of the
S2
accessory gene to down regulate in vivo replication without affecting in vitro growth properties. The results of these studies demonstrated that immunization with EIAV
UK
ΔS2 elicited mature virus-specific immune responses by 6 months and that this vaccine immunity provided protection from disease and detectable infection by intravenous challenge with a reference virulent biological clone, EIAV
PV
. This level of protection was observed in each of the six experimental horses challenged with the reference virulent EIAV
PV
by using a low-dose multiple-exposure protocol (three administrations of 10 median horse infectious doses [HID
50
], intravenous) designed to mimic field exposures and in all three experimentally immunized ponies challenged intravenously with a single inoculation of 3,000 HID
50
. In contrast, naïve equids subjected to the low- or high-dose challenge develop a detectable infection of challenge virus and acute disease within several weeks. Thus, these data demonstrate that the EIAV
S2
gene provides an optimal site for modification to achieve the necessary balance between attenuation to suppress virulence and replication potential to sufficiently drive host immune responses to produce vaccine immunity to viral exposure.
High-Frequency Genetic Recombination and Reactivation of Orthopoxviruses from DNA Fragments Transfected into Leporipoxvirus-Infected Cells
Authors: Yao Xiao-Dan , Evans David H. 
Published: June 2003

ABSTRACT

Poxvirus DNA is not infectious because establishing an infection requires the activities of enzymes packaged in the virion. This barrier can be overcome by transfecting virus DNA into cells previously infected with another poxvirus, since the resident virus can provide the
trans
-acting systems needed to reactivate transfected DNA. In this study we show that cells infected with a leporipoxvirus, Shope fibroma virus (SFV), can reactivate vaccinia virus DNA. Similar heterologous packaging systems which used fowlpox-infected cells to reactivate vaccinia virus have been described, but SFV-infected cells promoted a far more efficient reaction that can produce virus titers exceeding 10
6
PFU/μg of transfected DNA. SFV-promoted reactions also exploit the hyperrecombinogenic systems previously characterized in SFV-infected cells, and these coupled recombination and reactivation reactions could be used to delete nonessential regions of the vaccinia virus genome and to reconstruct vaccinia virus from overlapping DNA fragments. SFV-catalyzed recombination reactions need only two 18- to 20-bp homologies to target PCR amplicons to restriction enzyme-cut vaccinia virus vectors, and this reaction feature was used to rapidly clone and express a gene encoding fluorescent green protein without the need for plaque purification or selectable markers. The ability of SFV-infected cells to reactivate fragments of vaccinia virus was ultimately limited by the number of recombinational exchanges required and one cannot reconstruct vaccinia virus from multiple PCR fragments spanning essential portions of the genome. These observations suggest that recombination is an integral part of poxvirus reactivation reactions and provide a useful new technique for altering the structure of poxvirus genomes.
p21Waf1/Cip1/Sdi1Prevents Apoptosis as Well as Stimulates Growth in Cells Transformed or Immortalized by Human T-Cell Leukemia Virus Type 1-Encoded Tax
Authors: Kawata Sanae , Ariumi Yasuo , Shimotohno Kunitada 
Published: June 2003

ABSTRACTHuman T-cell leukemia virus type 1 (HTLV-1) Tax regulates the expression of virally encoded genes, as well as various endogenous host genes intrans. Tax-mediated regulation of gene expression is important for the immortalization of normal human T lymphocytes and the transformation of fibroblast cells, such as Rat-1 cells. Tax has the ability to transactivate p21Waf1/Cip1/Sdi1, resulting in high expression levels in HTLV-1-immortalized cells. Since p21 expression is suppressed due to methylation of the promoter region in Rat-l cell line, p21 may not be critical for the transformation of this cell line by Tax. To further understand the role of p21 for the proliferation of Tax-transformed Rat-1 cells, we examined the effect of ectopic expression of p21 in these cells. Here, we observed that p21 expression enhanced the transformation of this cell line via at least two mechanisms: (i) the enhancement of NF-κB activation and/or CREB signaling and (ii) the excitation of antiapoptotic machinery. To analyze the role of p21 that is overexpressed in HTLV-1-immortalized lymphocytes, p21 expression was suppressed by using an antisense oligonucleotide specific for p21 mRNA; these cells then became sensitive to apoptotic induction. These results suggest that p21 plays an important role in the proliferation of Tax-expressing cells through the regulation of at least two independent mechanisms.
Viability of Poliovirus/Rhinovirus VPg Chimeric Viruses and Identification of an Amino Acid Residue in the VPg Gene Critical for Viral RNA Replication
Authors: Cheney I. Wayne , Naim Suhaila , Shim Jae Hoon , Reinhardt Meghan , Pai Bharati , Wu Jim Z. , Hong Zhi , Zhong Weidong 
Published: June 2003

ABSTRACT

Picornaviral RNA replication utilizes a small virus-encoded protein, termed 3B or VPg, as a primer to initiate RNA synthesis. This priming step requires uridylylation of the VPg peptide by the viral polymerase protein 3D
pol
, in conjunction with other viral or host cofactors. In this study, we compared the viral specificity in 3D
pol
-catalyzed uridylylation reactions between poliovirus (PV) and human rhinovirus 16 (HRV16). It was found that HRV16 3D
pol
was able to uridylylate PV VPg as efficiently as its own VPg, but PV 3D
pol
could not uridylylate HRV16 VPg. Two chimeric viruses, PV containing HRV16 VPg (PV/R16-VPg) and HRV16 containing PV VPg (R16/PV-VPg), were constructed and tested for replication capability in H1-HeLa cells. Interestingly, only PV/R16-VPg chimeric RNA produced infectious virus particles upon transfection. No viral RNA replication or cytopathic effect was observed in cells transfected with R16/PV-VPg chimeric RNA, despite the ability of HRV16 3D
pol
to uridylylate PV VPg in vitro. Sequencing analysis of virion RNA isolated from the virus particles generated by PV/R16-VPg chimeric RNA identified a single residue mutation in the VPg peptide (Glu
6
to Val). Reverse genetics confirmed that this mutation was highly compensatory in enhancing replication of the chimeric viral RNA. PV/R16-VPg RNA carrying this mutation replicated with similar kinetics and magnitude to wild-type PV RNA. This cell culture-induced mutation in HRV16 VPg moderately increased its uridylylation by PV 3D
pol
in vitro, suggesting that it might be involved in other function(s) in addition to the direct uridylylation reaction. This study demonstrated the use of chimeric viruses to characterize viral specificity and compatibility in vivo between PV and HRV16 and to identify critical amino acid residue(s) for viral RNA replication.
Coexistence of Two Distinct Secretion Mutations (P5T and I97L) in Hepatitis B Virus Core Produces a Wild-Type Pattern of Secretion
Authors: Chua Pong Kian , Wen Yu-Mei , Shih Chiaho 
Published: June 2003

ABSTRACT
Unlike a Tokyo isolate of hepatitis B virus variants, we found a Shanghai isolate that secretes few virions with an immature genome despite its core I97L mutation. Core mutations P5T and I97L were found to be mutually compensatory in offsetting their respective distinct effects on virion secretion.
Replication-Competent Hybrids between Murine Leukemia Virus and Foamy Virus
Authors: Shikova-Lekova Evelina , Lindemann Dirk , Pietschmann Thomas , Juretzek Thomas , Rudolph Wolfram , Herchenröder Ottmar , Gelderblom Hans R. , Rethwilm Axel 
Published: June 2003

ABSTRACT

Replication-competent chimeric retroviruses constructed of members of the two subfamilies of
Retroviridae
, orthoretroviruses and spumaretroviruses, specifically murine leukemia viruses (MuLV) bearing hybrid MuLV-foamy virus (FV) envelope (
env
) genes, were characterized. All viruses had the cytoplasmic tail of the MuLV transmembrane protein. In ESL-1, a truncated MuLV leader peptide (LP) was fused to the complete extracellular portion of FV Env, and ESL-2 to -4 contained the complete MuLV-LP followed by N-terminally truncated FV Env decreasing in size. ESL-1 to -4 had an extended host cell range compared to MuLV, induced a cytopathology reminiscent of FVs, and exhibited an ultrastructure that combined the features of the condensed core of MuLV with the prominent surface knobs of FVs. Replication of ESL-2 to -4 resulted in the acquisition of a stop codon at the N terminus of the chimeric Env proteins. This mutation rendered the MuLV-LP nonfunctional and indicated that the truncated FV-LP was sufficient to direct Env synthesis into the secretory pathway. Compared to the parental viruses, the chimeras replicated with only moderate cell-free titers.
Establishment and Maintenance of Gammaherpesvirus Latency Are Independent of Infective Dose and Route of Infection
Authors: Tibbetts Scott A. , Loh Joy , van Berkel Victor , McClellan James S. , Jacoby Meagan A. , Kapadia Sharookh B. , Speck Samuel H. , Virgin Herbert W. 
Published: June 2003

ABSTRACT

Gammaherpesviruses such as Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus are important human pathogens that establish long-term latent infections. Understanding of the initiation and maintenance of latent infections has important implications for the prevention and treatment of gammaherpesvirus-related diseases. Although much is known about gammaherpesvirus pathogenesis, it is unclear how the infectious dose of a virus influences its ability to establish latent infection. To examine the relationship between the infectious dose and gammaherpesvirus latency, we inoculated wild-type mice with 0.01 to 10
6
PFU of murine gammaherpesvirus 68 (γHV68) and quantitatively measured latency and acute-phase replication. Surprisingly, during latency, the frequencies of ex vivo reactivation were similar over a 10
7
-fold range of doses for i.p. infection and over a 10
4
-fold range of doses for intranasal infection. Further, the frequencies of cells harboring viral genome during latency did not differ substantially over similar dose ranges. Although the kinetics of acute-phase replication were delayed at small doses of virus, the peak titer did not differ significantly between mice infected with a large dose of virus and those infected with a small dose of virus. The results presented here indicate that any initiation of infection leads to substantial acute-phase replication and subsequent establishment of a maximal level of latency. Thus, infections with doses as small as 0.1 PFU of γHV68 result in stable levels of acute-phase replication and latent infection. These results demonstrate that the equilibrium level of establishment of gammaherpesvirus latency is independent of the infectious dose and route of infection.
PORTFOLIO OPTIMIZATION OF SMALL SCALE FUND USING MEAN-ABSOLUTE DEVIATION MODEL
Authors: KONNO HIROSHI 
Published: June 2003

The purpose of this paper is to show that we are now able to apply standard portfolio optimization methods to the management of small and medium scale fund, where transaction cost and minimal transaction unit constraints are not negligible. Unit transaction cost is usually larger when the amount of investment is smaller. Also, rounding of portfolio to the nearest integer multiple of minimal transaction unit will have non negligible effect on the risk-return structure of the portfolio. We will show that the use of mean-absolute deviation model enables one to handle concave transaction cost and minimal transaction unit constraints in an efficient manner using branch and bound algorithm. Also, we will show that the minimal transaction cost rebalancing problem can be solved by using the same algorithm.
‘On-Line’ Alterations of Contralateral Jugular Blood Gas Profile during Carotid Clamping
Authors: Vretzakis G. , Papadimitriou D. , Papaziogas B. , Koutsias S. , Christopoulos D. , Ferdi E. , Papadopoulos G. 
Published: June 2003

The aim of this work was to record the metabolic status of the brain (pH, PCO<sub>2</sub> and PO<sub>2</sub>) during carotid endarterectomy (CEA), with the use of an intravascular multiparameter sensor (Paratrend 7) via retrograde catheterization of the contralateral jugular vein. Twenty-four patients with ASA grades II and III scheduled for CEA were included in the study. After induction of anesthesia, the contralateral internal jugular vein was punctured retrogradely and the sensor was introduced. During clamping, pH became persistently more acidotic (7.34–7.31; p < 0.05), PCO<sub>2</sub> was elevated (43.2–46.8 mm Hg; p < 0.05) while most of the patients showed a non-significant decrease in PjvO<sub>2</sub>/SjvO<sub>2</sub> (jv = jugular venous). Correlation with clamping time or stump pressure was not significant. Unclamping was followed by a short period (5– 9 min) of decrease in pH and elevation of PCO<sub>2</sub> (7.30–7.22; p < 0.05, and 48.0–52.5 mm Hg; p < 0.05, respectively). PjvO<sub>2</sub> was significantly elevated (51.8–58.0 mm Hg; p < 0.001) after the restoration of flow. The study suggests that local CO<sub>2</sub> creates conditions for compensation of flow after the application of a carotid clamp. We consider that this monitoring technique, after further validation, may provide useful information.
The Serum Cortisol:Cortisone Ratio in the Postoperative Acute-Phase Response
Authors: Vogeser M. , Groetzner J. , Küpper C. , Briegel J. 
Published: June 2003

<i>Objective:</i> In a previous cross-sectional pilot investigation, an increase in the ratio of active cortisol to inactive cortisone in serum has been found as a general phenomenon during the acute-phase response. The aim of the present study was to further characterize this alteration of cortisol metabolism in patients undergoing elective cardiac bypass surgery. <i>Methods:</i> Cortisol and cortisone were quantified by use of liquid-chromatography tandem mass spectrometry in sera that were sampled preoperatively and on the first 4 postoperative days (POD) from 16 patients undergoing aortocoronary bypass grafting (7.00 a.m.). <i>Results:</i> The median serum cortisol concentration peaked on the first POD and then decreased statistically significantly until the end of the observation period: preoperatively, 245 nmol/l (IQR 198–331); 1st POD, 532 nmol/l (IQR 409–678 ); 4th POD, 373 nmol/l (IQR 306–493); p for trend = 0.019. In contrast, the cortisol:cortisone ratio was constantly increased approximately twofold on all POD compared to preoperative sampling: preoperatively, 5.4 (IQR 5.0–7.2); 1st POD, 11.3 (IQR 9.2–13.6); 4th POD, 9.9 (IQR 7.7–11.0), with no significant trend of normalization. <i>Conclusion:</i> Following major surgery, the substantial increase in the serum cortisol:cortisone ratio – reflecting a shift in the overall set-point of 11β-hydroxysteroid dehydrogenase activity – is more sustained than the increase in serum cortisol; the increase in the cortisol:cortisone ratio seems to be a long-term phenomenon of the activation of the hypothalamic-pituitary-adrenocortical system by surgical stress and systemic inflammation.