bluuebunny/crossref_metadata_2025 huggingface dataset:
A postgenomic method for predicting essential genes at subsaturation levels of mutagenesis: Application to
Mycobacterium tuberculosis
Authors: Lamichhane Gyanu , Zignol Matteo , Blades Natalie J. , Geiman Deborah E. , Dougherty Annette , Grosset Jacques , Broman Karl W. , Bishai William R.
Published: June 2003

We describe a postgenomic
in silico
approach for identifying genes that are likely to be essential and estimate their proportion in haploid genomes. With the knowledge of all sites eligible for mutagenesis and an experimentally determined partial list of nonessential genes from genome mutagenesis, a Bayesian statistical method provides reasonable predictions of essential genes with a subsaturation level of random mutagenesis. For mutagenesis, a transposon such as
Himar1
is suitable as it inserts randomly into TA sites. All of the possible insertion sites may be determined
a priori
from the genome sequence and with this information, data on experimentally hit TA sites may be used to predict the proportion of genes that cannot be mutated. As a model, we used the
Mycobacterium tuberculosis
genome. Using the
Himar1
transposon, we created a genetically defined collection of 1,425 insertion mutants. Based on our Bayesian statistical analysis using Markov chain Monte Carlo and the observed frequencies of transposon insertions in all of the genes, we estimated that the
M. tuberculosis
genome contains 35% (95% confidence interval, 28%–41%) essential genes. This analysis further revealed seven functional groups with high probabilities of being enriched in essential genes. The PE-PGRS (Pro-Glu polymorphic GC-rich repetitive sequence) family of genes, which are unique to mycobacteria, the polyketide/nonribosomal peptide synthase family, and mycolic and fatty acid biosynthesis gene families were disproportionately enriched in essential genes. At subsaturation levels of mutagenesis with a random transposon such as
Himar1
, this approach permits a statistical prediction of both the proportion and identities of essential genes of sequenced genomes.
In vivo
two-photon calcium imaging of neuronal networks
Authors: Stosiek Christoph , Garaschuk Olga , Holthoff Knut , Konnerth Arthur
Published: June 2003

Two-photon calcium imaging is a powerful means for monitoring the activity of distinct neurons in brain tissue
in vivo
. In the mammalian brain, such imaging studies have been restricted largely to calcium recordings from neurons that were individually dye-loaded through microelectrodes. Previous attempts to use membrane-permeant forms of fluorometric calcium indicators to load populations of neurons have yielded satisfactory results only in cell cultures or in slices of immature brain tissue. Here we introduce a versatile approach for loading membrane-permeant fluorescent indicator dyes in large populations of cells. We established a pressure ejection-based local dye delivery protocol that can be used for a large spectrum of membrane-permeant indicator dyes, including calcium green-1 acetoxymethyl (AM) ester, Fura-2 AM, Fluo-4 AM, and Indo-1 AM. We applied this dye-loading protocol successfully in mouse brain tissue at any developmental stage from newborn to adult
in vivo
and
in vitro. In vivo
two-photon Ca
2+
recordings, obtained by imaging through the intact skull, indicated that whisker deflection-evoked Ca
2+
transients occur in a subset of layer 2/3 neurons of the barrel cortex. Thus, our results demonstrate the suitability of this technique for real-time analyses of intact neuronal circuits with the resolution of individual cells.
Transcriptome signature of irreversible senescence in human papillomavirus-positive cervical cancer cells
Authors: Wells Susanne I. , Aronow Bruce J. , Wise Trisha M. , Williams Sarah S. , Couget Jennifer A. , Howley Peter M.
Published: June 2003

A frequent characteristic of human papillomavirus (HPV)-positive cervical cancers is the loss of viral E2 gene expression in HPV-infected cervical epithelial cells as a consequence of viral DNA integration into the cellular genome. The expression of E2 in HPV-positive cancer cells results in the repression of the viral E6/E7 oncogenes, activation of the p53 and pRB pathways, and a G
1
cell cycle arrest, followed by induction of cellular senescence. The transcriptional consequences of E2-mediated cell cycle arrest that lead to senescence currently are unknown. Using conditional senescence induction in HeLa cells and microarray analysis, we describe here the expression profile of cells irreversibly committed to senescence. Our results provide insight into the molecular anatomy of senescence pathways and its regulation by HPV on-coproteins. These include the induction of the RAB vesicular transport machinery and a general down-regulation of chromatin regulatory molecules. The repression of tumor-specific G antigens during E2 senescence supports a reversal of the tumorigenic phenotype by E2 and the potential approach of tumor-specific G antigen-specific immunotherapy for cervical cancer.
Purifying mRNAs with a high-affinity eIF4E mutant identifies the short 3′ poly(A) end phenotype
Authors: Choi Youkyung Hwang , Hagedorn Curt H.
Published: June 2003

The use of DNA microarrays has revolutionized the manner in which mRNA populations are analyzed. One limitation of the current technology is that mRNAs are often purified on the basis of their 3′ poly(A) ends, which can be extremely short or absent in some mRNAs. To circumvent this limitation, we have developed a procedure for the purification of eukaryotic mRNAs using a mutant version of the mRNA 5′ cap-binding protein (eIF4E) with increased affinity for the m
7
GTP moiety of the cap. By using this procedure, we have compared the populations of mammalian mRNAs purified by oligo(dT) and 5′ cap selection with oligonucleotide microarrays. This analysis has identified a subpopulation of mRNAs that are present with short 3′ poly(A) ends at steady state and are missed or underrepresented after purification by oligo(dT). These mRNAs may respond to specific posttranscriptional control mechanisms such as cytoplasmic polyadenylation.
Recombineering with overlapping single-stranded DNA oligonucleotides: Testing a recombination intermediate
Authors: Yu Daiguan , Sawitzke James A. , Ellis Hilary , Court Donald L.
Published: June 2003

A phage λ-based recombination system, Red, can be used for high-efficiency mutagenesis, repair, and engineering of chromosomal or episomal DNA
in vivo
in
Escherichia coli
. When long linear double-stranded DNA with short flanking homologies to their targets are used for the recombination, the λ Exo, Beta, and Gam proteins are required. The current model is: (
i
) Gam inhibits the host RecBCD activity, thereby protecting the DNA substrate for recombination; (
ii
) Exo degrades from each DNA end in a 5′ → 3′ direction, creating double-stranded DNA with 3′ single-stranded DNA tails; and (
iii
) Beta binds these 3′ overhangs to protect and anneal them to complementary sequences. We have tested this model for Red recombination by using electroporation to introduce overlapping, complementary oligonucleotides that when annealed
in vivo
approximate the recombination intermediate that Exo should create. Using this technique we found Exo-independent recombination. Surprisingly, a similarly constructed substrate with 5′ overhangs recombined more efficiently. This 5′ overhang recombination required both Exo and Beta for high levels of recombination and the two oligonucleotides need to overlap by only 6 bp on their 3′ ends. Results indicate that Exo may load Beta onto the 3′ overhang it produces. In addition, multiple overlapping oligonucleotides were successfully used to generate recombinants
in vivo
, a technique that could prove useful for many genetic engineering procedures.
Aberrant lamination in the cerebral cortex of mouse embryos lacking DNA topoisomerase IIβ
Authors: Lyu Yi Lisa , Wang James C.
Published: June 2003

We have examined corticogenesis in mouse embryos lacking DNA topoisomerase IIβ (IIβ) in the brain or in all tissues. The absence of IIβ, a type II DNA topoisomerase normally expressed in postmitotic cells in the developing cortex, severely affects cerebral stratification: no subplate is discernible, and neurons born at later stages of corticogenesis fail to migrate to the superficial layers. This abnormal pattern of neuron positioning in the cerebral cortex is reminiscent of that observed in mouse mutants defective in the reelin-signaling pathway. Significantly, the level of reelin in the neocortex is much reduced when IIβ is absent. These results implicate a role of IIβ in brain development. The enzyme may be required in implementing particular genetic programs in postmitotic cells, such as reelin expression in Cajal-Retzius cells, perhaps through its action on nucleoprotein structure of particular chromosomal regions.
Crystal structure of a bifunctional aldolase–dehydrogenase: Sequestering a reactive and volatile intermediate
Authors: Manjasetty Babu A. , Powlowski Justin , Vrielink Alice
Published: June 2003

The crystal structure of the bifunctional enzyme 4-hydroxy-2-ketovalerate aldolase (DmpG)/acylating acetaldehyde dehydrogenase (DmpF), which is involved in the bacterial degradation of toxic aromatic compounds, has been determined by multiwavelength anomalous dispersion (MAD) techniques and refined to 1.7-Å resolution. Structures of the two polypeptides represent a previously unrecognized subclass of metal-dependent aldolases, and of a CoA-dependent dehydrogenase. The structure reveals a mixed state of NAD
+
binding to the DmpF protomer. Domain movements associated with cofactor binding in the DmpF protomer may be correlated with channeling and activity at the DmpG protomer. In the presence of NAD
+
a 29-Å-long sequestered tunnel links the two active sites. Two barriers are visible along the tunnel and suggest control points for the movement of the reactive and volatile acetaldehyde intermediate between the two active sites.
Probucol prevents early coronary heart disease and death in the high-density lipoprotein receptor SR-BI/apolipoprotein E double knockout mouse
Authors: Braun Anne , Zhang Songwen , Miettinen Helena E. , Ebrahim Shamsah , Holm Teresa M. , Vasile Eliza , Post Mark J. , Yoerger Danita M. , Picard Michael H. , Krieger Joshua L. , Andrews Nancy C. , Simons Michael , Krieger Monty
Published: June 2003

Mice with homozygous null mutations in the high-density lipoprotein receptor SR-BI (scavenger receptor class B, type I) and apolipoprotein E genes fed a low-fat diet exhibit a constellation of pathologies shared with human atherosclerotic coronary heart disease (CHD): hypercholesterolemia, occlusive coronary atherosclerosis, myocardial infarctions, cardiac dysfunction (heart enlargement, reduced systolic function and ejection fraction, and ECG abnormalities), and premature death (mean age 6 weeks). They also exhibit a block in RBC maturation and abnormally high plasma unesterified-to-total cholesterol ratio (0.8) with associated abnormal lipoprotein morphology (lamellar/vesicular and stacked discoidal particles reminiscent of those in lecithin/cholesterol acyltransferase deficiency and cholestasis). Treatment with the lipid-lowering, antiatherosclerosis, and antioxidation drug probucol extended life to as long as 60 weeks (mean 36 weeks), and at 5–6 weeks of age, virtually completely reversed the cardiac and most RBC pathologies and corrected the unesterified to total cholesterol ratio (0.3) and associated distinctive abnormal lipoprotein morphologies. Manipulation of the timing of administration and withdrawal of probucol could control the onset of death and suggested that critical pathological changes usually occurred in untreated double knockout mice between ≈3 (weaning) and 5 weeks of age and that probucol delayed heart failure even after development of substantial CHD. The ability of probucol treatment to modulate pathophysiology in the double knockout mice enhances the potential of this murine system for analysis of the pathophysiology of CHD and preclinical testing of new approaches for the prevention and treatment of cardiovascular disease.
Cu/Zn superoxide dismutase mutants associated with amyotrophic lateral sclerosis show enhanced formation of aggregates
in vitro
Authors: Stathopulos P. B. , Rumfeldt J. A. O. , Scholz G. A. , Irani R. A. , Frey H. E. , Hallewell R. A. , Lepock J. R. , Meiering E. M.
Published: June 2003

Mutations in Cu/Zn superoxide dismutase (SOD) are associated with the fatal neurodegenerative disorder amyotrophic lateral sclerosis (ALS). There is considerable evidence that mutant SOD has a gain of toxic function; however, the mechanism of this toxicity is not known. We report here that purified SOD forms aggregates
in vitro
under destabilizing solution conditions by a process involving a transition from small amorphous species to fibrils. The assembly process and the tinctorial and structural properties of the
in vitro
aggregates resemble those for aggregates observed
in vivo
. Furthermore, the familial ALS SOD mutations A4V, G93A, G93R, and E100G decrease protein stability, which correlates with an increase in the propensity of the mutants to form aggregates. These mutations also increase the rate of protein unfolding. Our results suggest three possible mechanisms for the increase in aggregation: (
i
) an increase in the equilibrium population of unfolded or of partially unfolded states, (
ii
) an increase in the rate of unfolding, and (
iii
) a decrease in the rate of folding. Our data support the hypothesis that the gain of toxic function for many different familial ALS-associated mutant SODs is a consequence of protein destabilization, which leads to an increase in the formation of cytotoxic protein aggregates.
A Reversible Defect in Natural Killer T Cell Function Characterizes the Progression of Premalignant to Malignant Multiple Myeloma
Authors: Dhodapkar Madhav V. , Geller Matthew D. , Chang David H. , Shimizu Kanako , Fujii Shin-Ichiro , Dhodapkar Kavita M. , Krasovsky Joseph
Published: June 2003

We studied the function of antitumor T and natural killer T (NKT) cells from the blood and tumor bed in 23 patients with premalignant gammopathy, nonprogressive myeloma, or progressive multiple myeloma. We show that antitumor killer T cells can be detected in patients with both progressive or nonprogressive myeloma. Vα24+Vβ11+ invariant NKT cells are detectable in the blood and tumor bed of all cohorts. However, freshly isolated NKT cells from both the blood and tumor bed of patients with progressive disease, but not nonprogressive myeloma or premalignant gammopathy, have a marked deficiency of ligand-dependent interferon-γ production. This functional defect can be overcome in vitro using dendritic cells pulsed with the NKT ligand, α-galactosylceramide (α-GalCer). Fresh myeloma cells express CD1d, and can be efficiently killed by autologous NKT cells. We hypothesize that presentation of tumor derived glycolipids by myeloma cells leads to NKT dysfunction in vivo. These data demonstrate that clinical progression in patients with monoclonal gammopathies is associated with an acquired but potentially reversible defect in NKT cell function and support the possibility that these innate lymphocytes play a role in controlling the malignant growth of this incurable B cell tumor in patients.
Boosting for tumor classification with gene expression data
Authors: Dettling Marcel , Bühlmann Peter
Published: June 2003

Motivation: Microarray experiments generate large datasets with expression values for thousands of genes but not more than a few dozens of samples. Accurate supervised classification of tissue samples in such high-dimensional problems is difficult but often crucial for successful diagnosis and treatment. A promising way to meet this challenge is by using boosting in conjunction with decision trees.

Results: We demonstrate that the generic boosting algorithm needs some modification to become an accurate classifier in the context of gene expression data. In particular, we present a feature preselection method, a more robust boosting procedure and a new approach for multi-categorical problems. This allows for slight to drastic increase in performance and yields competitive results on several publicly available datasets.

Availability: Software for the modified boosting algorithms as well as for decision trees is available for free in R at http://stat.ethz.ch/~dettling/boosting.html

Contact: dettling@stat.math.ethz.ch

* To whom correspondence should be addressed.
Coupled two-way clustering analysis of breast cancer and colon cancer
gene expression data
Authors: Getz Gad , Gal Hilah , Kela Itai , Notterman Daniel A. , Domany Eytan
Published: June 2003

We present and review coupled two-way clustering, a method designed to mine gene expression data. The method identifies submatrices of the total expression matrix, whose clustering analysis reveals partitions of samples (and genes) into biologically relevant classes. We demonstrate, on data from colon and breast cancer, that we are able to identify partitions that elude standard clustering analysis

Availability: Free, at http://ctwc.weizmann.ac.il

Contact: eytan.domany@weizmann.ac.il

Supplementary information: http://www.weizmann.ac.il/physics/complex/compphys/bioinfo2/

* To whom correspondence should be addressed.
Modified nonparametric approaches to detecting differentially
expressed genes in replicated microarray experiments
Authors: Zhao Yanli , Pan Wei
Published: June 2003

Motivation: An important goal in analyzing microarray data is to determine which genes are differentially expressed across two kinds of tissue samples or samples obtained under two experimental conditions. Various parametric tests, such as the two-sample t-test, have been used, but their possibly too strong parametric assumptions or large sample justifications may not hold in practice. As alternatives, a class of three nonparametric statistical methods, including the empirical Bayes method of Efron et al. (2001), the significance analysis of microarray (SAM) method of Tusher et al. (2001) and the mixture model method (MMM) of Pan et al. (2001), have been proposed. All the three methods depend on constructing a test statistic and a so-called null statistic such that the null statistic’s distribution can be used to approximate the null distribution of the test statistic. However, relatively little effort has been directed toward assessment of the performance or the underlying assumptions of the methods in constructing such test and null statistics

Results: We point out a problem of a current method to construct the test and null statistics, which may lead to largely inflated Type I errors (i.e. false positives). We also propose two modifications that overcome the problem. In the context of MMM, the improved performance of the modified methods is demonstrated using simulated data. In addition, our numerical results also provide evidence to support the utility and effectiveness of MMM

Contact: weip@biostat.umn.edu

* To whom correspondence should be addressed.
A statistical problem for inference to regulatory
structure from associations of gene expression measurements with
microarrays
Authors: Chu Tianjiao , Glymour Clark , Scheines Richard , Spirtes Peter
Published: June 2003

Motivation: One approach to inferring genetic regulatory structure from microarray measurements of mRNA transcript hybridization is to estimate the associations of gene expression levels measured in repeated samples. The associations may be estimated by correlation coefficients or by conditional frequencies (for discretized measurements) or by some other statistic. Although these procedures have been successfully applied to other areas, their validity when applied to microarray measurements has yet to be tested

Results: This paper describes an elementary statistical difficulty for all such procedures, no matter whether based on Bayesian updating, conditional independence testing, or other machine learning procedures such as simulated annealing or neural net pruning. The difficulty obtains if a number of cells from a common population are aggregated in a measurement of expression levels. Although there are special cases where the conditional associations are preserved under aggregation, in general inference of genetic regulatory structure based on conditional association is unwarranted

Contact: tchu@andrew.cmu.edu

* To whom correspondence should be addressed.
Bagging to improve the accuracy of a clustering procedure
Authors: Dudoit Sandrine , Fridlyand Jane
Published: June 2003

Motivation: The microarray technology is increasingly being applied in biological and medical research to address a wide range of problems such as the classification of tumors. An important statistical question associated with tumor classification is the identification of new tumor classes using gene expression profiles. Essential aspects of this clustering problem include identifying accurate partitions of the tumor samples into clusters and assessing the confidence of cluster assignments for individual samples.

Results: Two new resampling methods, inspired from bagging in prediction, are proposed to improve and assess the accuracy of a given clustering procedure. In these ensemble methods, a partitioning clustering procedure is applied to bootstrap learning sets and the resulting multiple partitions are combined by voting or the creation of a new dissimilarity matrix. As in prediction, the motivation behind bagging is to reduce variability in the partitioning results via averaging. The performances of the new and existing methods were compared using simulated data and gene expression data from two recently published cancer microarray studies. The bagged clustering procedures were in general at least as accurate and often substantially more accurate than a single application of the partitioning clustering procedure. A valuable by-product of bagged clustering are the cluster votes which can be used to assess the confidence of cluster assignments for individual observations

Contact: sandrine@stat.berkeley.edu

Supplementary information: For supplementary information on datasets, analyses, and software, consult http://www.stat.berkeley.edu/~sandrine and http://www.bioconductor.org.

* To whom correspondence should be addressed.   The authors wish it to be known that, in their opinion, both authors should be regarded as joint First Authors.
Simultaneous gene clustering and subset selection for sample classification via MDL
Authors: Jörnsten Rebecka , Yu Bin
Published: June 2003

Motivation: The microarray technology allows for the simultaneous monitoring of thousands of genes for each sample. The high-dimensional gene expression data can be used to study similarities of gene expression profiles across different samples to form a gene clustering. The clusters may be indicative of genetic pathways. Parallel to gene clustering is the important application of sample classification based on all or selected gene expressions. The gene clustering and sample classification are often undertaken separately, or in a directional manner (one as an aid for the other). However, such separation of these two tasks may occlude informative structure in the data. Here we present an algorithm for the simultaneous clustering of genes and subset selection of gene clusters for sample classification. We develop a new model selection criterion based on Rissanen’s MDL (minimum description length) principle. For the first time, an MDL code length is given for both explanatory variables (genes) and response variables (sample class labels). The final output of the proposed algorithm is a sparse and interpretable classification rule based on cluster centroids or the closest genes to the centroids

Results: Our algorithm for simultaneous gene clustering and subset selection for classification is applied to three publicly available data sets. For all three data sets, we obtain sparse and interpretable classification models based on centroids of clusters. At the same time, these models give competitive test error rates as the best reported methods. Compared with classification models based on single gene selections, our rules are stable in the sense that the number of clusters has a small variability and the centroids of the clusters are well correlated (or consistent) across different cross validation samples. We also discuss models where the centroids of clusters are replaced with the genes closest to the centroids. These models show comparable test error rates to models based on single gene selection, but are more sparse as well as more stable. Moreover, we comment on how the inclusion of a classification criterion affects the gene clustering, bringing out class informative structure in the data

Availability: The methods presented in this paper have been implemented in the R language. The source code is available from the first author.

Contact: rebecka@stat.rutgers.edu

* To whom correspondence should be addressed.
Modular modeling of cellular systems with ProMoT/Diva
Authors: Ginkel M. , Kremling A. , Nutsch T. , Rehner R. , Gilles E. D.
Published: June 2003

Motivation: Need for software to setup and analyze complex mathematical models for cellular systems in a modular way, that also integrates the experimental environment of the cells

Results: A computer framework is described which allows the building of modularly structured models using an abstract, modular and general modeling methodology. With this methodology, reusable modeling entities are introduced which lead to the development of a modeling library within the modeling tool ProMot. The simulation environment Diva is used for numerical analysis and parameter identification of the models. The simulation environment provides a number of tools and algorithms to simulate and analyze complex biochemical networks. The described tools are the first steps towards an integrated computer-based modeling, simulation and visualization environment

Availability: Available on request to the authors. The software itself is free for scientific purposes but requires commercial libraries

Contact: ginkel@mpi-magdeburg.mpg.de

Supplementary information: http://www.mpi-magdeburg.mpg.de/projects/promot

* To whom correspondence should be addressed.
eXPatGen: generating dynamic expression patterns
for the systematic evaluation of analytical methods
Authors: Michaud Dennis J. , Marsh Adam G. , Dhurjati Prasad S.
Published: June 2003

Motivation: Experimental gene expression data sets, such as those generated by microarray or gene chip experiments, typically have significant noise and complicated interconnectivities that make understanding even simple regulatory patterns difficult. Given these complications, characterizing the effectiveness of different analysis techniques to uncover network groups and structures remains a challenge. Generating simulated expression patterns with known biological features of expression complexity, diversity and interconnectivities provides a more controlled means of investigating the appropriateness of different analysis methods. A simulation-based approach can systematically evaluate different gene expression analysis techniques and provide a basis for improved methods in dynamic metabolic network reconstruction

Results: We have developed an on-line simulator, called eXPatGen, to generate dynamic gene expression patterns typical of microarray experiments. eXPatGen provides a quantitative network structure to represent key biological features, including the induction, repression, and cascade regulation of messenger RNA (mRNA). The simulation is modular such that the expression model can be replaced with other representations, depending on the level of biological detail required by the user. Two example gene networks, of 25 and 100 genes respectively, were simulated. Two standard analysis techniques, clustering and PCA analysis, were performed on the resulting expression patterns in order to demonstrate how the simulator might be used to evaluate different analysis methods and provide experimental guidance for biological studies of gene expression

Availability: http://www.che.udel.edu/eXPatGen/

Contact: dhurjati@che.udel.edu

* To whom correspondence should be addressed.
RASCAL: rapid scanning and correction of multiple sequence alignments
Authors: Thompson J. D. , Thierry J. C. , Poch O.
Published: June 2003

Motivation: Most multiple sequence alignment programs use heuristics that sometimes introduce errors into the alignment. The most commonly used methods to correct these errors use iterative techniques to maximize an objective function. We present here an alternative, knowledge-based approach that combines a number of recently developed methods into a two-step refinement process. The alignment is divided horizontally and vertically to form a‘ lattice’ in which well aligned regions can be differentiated. Alignment correction is then restricted to the less reliable regions, leading to a more reliable and efficient refinement strategy

Results: The accuracy and reliability of RASCAL is demonstrated using: (i) alignments from the BAliBASE benchmark database, where significant improvements were often observed, with no deterioration of the existing high-quality regions, (ii) a large scale study involving 946 alignments from the ProDom protein domain database, where alignment quality was increased in 68% of the cases; and (iii) an automatic pipeline to obtain a high-quality alignment of 695 full-length nuclear receptor proteins, which took 11 min on a DEC Alpha 6100 computer

Availability: RASCAL is available at ftp://ftp-igbmc.u-strasbg.fr/pub/RASCAL

Contact: poch@igbmc.u-strasbg.fr

Supplementary information: http://bioinfo-igbmc.u-strasbourg.fr/BioInfo/RASCAL/paper/rascal_supp.html

* To whom correspondence should be addressed.
Transcription-dependent recombination and the role of fork collision in yeast rDNA
Authors: Takeuchi Yasushi , Horiuchi Takashi , Kobayashi Takehiko
Published: June 2003

It is speculated that the function of the replication fork barrier (RFB) site is to avoid collision between the 35S rDNA transcription machinery and the DNA replication fork, because the RFB site is located near the 3′-end of the gene and inhibits progression of the replication fork moving in the opposite direction to the transcription machinery. However, the collision has never been observed in a blockless (fob1) mutant with 150 copies of rDNA. The geneFOB1was shown previously to be required for replication fork blocking activity at the RFB site, and also for the rDNA copy number variation through unequal sister-chromatid recombination. This study documents the detection of fork collision in anfob1derivative with reduced rDNA copy number (∼20) using two-dimensional agarose gel electrophoresis. This suggests that most of these reduced copies are actively transcribed. The collision was dependent on the transcription by RNA polymerase I. In addition, the transcription stimulated rDNA copy number variation, and the production of the extrachromosomal rDNA circles (ERCs), whose accumulation is thought to be a cause of aging. These results suggest that such a transcription-dependent fork collision induces recombination, and may function as a general recombination trigger for multiplication of highly transcribed single-copy genes.
Elimination of Mcl-1 is required for the initiation of apoptosis following ultraviolet irradiation
Authors: Nijhawan Deepak , Fang Min , Traer Elie , Zhong Qing , Gao Wenhua , Du Fenghe , Wang Xiaodong
Published: June 2003

Ultraviolet (UV) irradiation of HeLa cells triggers an apoptotic response mediated by mitochondria. Biochemical analysis of this response revealed that the elimination of cytosolic inhibitors is required for mitochondrial release of cytochromecand subsequent caspase activation. These inhibitors were found to be Mcl-1 and Bcl-xL, two antiapoptotic members of the Bcl-2 family. Following UV treatment, Mcl-1 protein synthesis is blocked, the existing pool of Mcl-1 protein is rapidly degraded by the proteasome, and cytosolic Bcl-xLtranslocates to the mitochondria. These events are sequential; the elimination of Mcl-1 is required for the translocation of Bcl-xL. The disappearance of Mcl-1 is also required for other mitochondrial apoptotic events including Bax translocation, cytochromecrelease, and caspase activation.
Control of landmark events in meiosis by the CDK Cdc28 and the meiosis-specific kinase Ime2
Authors: Benjamin Kirsten R. , Zhang Chao , Shokat Kevan M. , Herskowitz Ira
Published: June 2003

Meiosis is thought to require the protein kinase Ime2 early for DNA replication and the cyclin-dependent kinase Cdc28 late for chromosome segregation. To elucidate the roles of these kinases, we inhibited their activities early and late using conditional mutants that are sensitive to chemical inhibitors. Our studies reveal that both Cdc28 and Ime2 have critical roles in meiotic S phase and M phase. Early inhibition of analog-sensitivecdc28-as1blocked DNA replication, revealing a previously undetected role for Cdc28. Yet Cdc28 was dispensable for one of its functions in the mitotic cell cycle, degradation of Sic1. Late addition of inhibitor toime2-as1revealed unexpected roles of Ime2 in the initiation and execution of chromosome segregation. The requirement of Ime2 for M phase is partially explained by its stimulation of the key meiotic transcription factor Ndt80, which is needed in turn for high Cdc28 activity. In accordance with a late role for Ime2, we observed an increase in its activity during M phase that depended on Cdc28 and Ndt80. We speculate that several unique features of the meiotic cell division reflect a division of labor and regulatory coordination between Ime2 and Cdc28.
The turnover of jobs and workers in a deep recession: evidence from the Finnish business sector
Authors: Ilmakunnas Pekka , Maliranta Mika
Published: June 2003

Job and worker flows in the Finnish business sector are studied during a deep recession in the early 1990s. The data set covers effectively the whole work force. The gross job and worker flow rates are fairly high. The evidence suggests that the adjustment of labor input has happened through a reduced hiring rate rather than through an increased separation rate. However, during the recession the group of declining plants included more and larger plants than before, which led to reduced employment. Excess worker turnover (churning) and excess job reallocation have been low during the recession. The evidence of the countercyclicality of job reallocation is mixed. The flows are calculated both for the whole business sector, and for seven main industries. Services have clearly higher flow rates than manufacturing, but the cyclical changes in the flows are fairly similar in all industries. To test the sensitivity of the results to data sources, job flows are calculated from three different statistics.
Productivity and wage effects of “family‐friendly” fringe benefits
Authors: Baughman Reagan , DiNardi Daniela , Holtz‐Eakin Douglas
Published: June 2003

Family‐supportive employment benefits have become increasingly popular in recent years as an employer response to the increasing labor force participation of women, and the consequent need to balance work and family life. Economic theory predicts that these types of fringe benefits could at least partially pay for themselves through a combination of increased productivity and lower wages. A survey of 120 employers in an upstate New York county provides data on benefits packages and outcome measures that are used to test this hypothesis. We find that employers who offer flexible sick leave and child care assistance experience measurable reductions in turnover. Employers who offer benefits like flexible scheduling policies and child care also appear to offset part of the cost of these benefits by paying lower entry‐level wages than do their competitors.
Human resource costs and benefits of maintaining a mature‐age workforce
Authors: Brooke Libby
Published: June 2003

The global trend of an ageing workforce and government policy directions towards reversing early retirement trends raises the issue of the costs to employers of an older workforce. Data on older workers human resources costs are lacking generally in Australia and other countries. This analysis of human resource costs and benefits relies on aggregate Australia national human resources benchmarking data that are applied to older workers. The study is based on the ratio of duration of employment of older workers compared to younger workers and uses this ratio as a multiplier of human resource costs. The analysis considers recruitment, training, absenteeism and work injuries of older compared to younger workers. The analysis found that net benefits occurred through recruitment and training benefits over the costs of absenteeism and work injuries. Further non‐quantified benefits of older workers identified in international case studies are also explained. These quantified and non‐quantified benefits of older workers suggest that identified positive inducements to employers exist which support human resources investments in older workers.
Dispositional traits and turnover intention
Authors: Chiu Randy K. , Francesco Anne Marie
Published: June 2003

This paper investigates the relationships between turnover intention and positive affectivity (PA) and negative affectivity (NA), and the mediating roles of job satisfaction and affective commitment in those relationships. Based on a sample of 279 Chinese managers, PA predicts turnover intention, and job satisfaction mediates the relationship. However, NA is neither directly nor indirectly related to turnover intention.
Using an HRM pattern approach to examine the productivity of manufacturing firms – an empirical study
Authors: Chen Liang‐Hsuan , Liaw Shu‐Yi , Lee Tzai‐Zang
Published: June 2003

Manufacturing firms are always faced with the problem of promoting operational performance and labor‐force management. The utilization of human resources is closely correlated with operations and production performance. This study investigates the correlation between human resource management (HRM) and business performance of large‐scale manufacturing firms in Taiwan. First, 16 subjects of HRM are designed to survey the importance level and achievement level of HRM by the sample firms. Productivity indices are also defined to measure business performance. Based on the survey, four critical HRM factors including 12 subjects are extracted by factor analysis. The difference between importance level and achievement level of subjects contained in each factor is examined. Furthermore, considering importance and achievement levels of HRM as features, fuzzy clustering analysis is employed to categorize the firms into four patterns. With various HRM characteristics, each pattern has different business performance in terms of productivity. Using a pattern approach, these findings can aid the firms in each pattern to improve their productivity by improving their HRM strategies.
Individual article supply: some strategic directions
Authors: Rowse Mark
Published: June 2003

Examines the increase in individual article supply and the resultant effects on journal subscriptions and site licensing, noting that pressure on library budgets has resulted in subscription cancellations but an increase in separates ordering, via document delivery and interlibrary loan (ILL). Increasingly sophisticated search and navigation tools enable users to navigate from a variety of primary, secondary and tertiary resources directly to an article – regardless of where the article is hosted or by which vendor it is sold. The implications for all the participants in the scholarly communications chain are examined and some pertinent questions are asked, including: does individual article supply erode existing publisher business; does the big (consortia) deal provide more value; and is ILL the most economical form of individual article supply? Concludes that both publishers and libraries must re‐examine their business models to counteract end‐users seeking freely available Web‐based or e‐print material, which is undermining the traditional, peer‐reviewed, scholarly communications process.
An institution in change: a private institution in transition
Authors: McRoy Ian , Gibbs Paul
Published: June 2003

This paper considers the issues facing an institution as it confronts the transition from college to university. Utilizing insights from the UK experience of polytechnics moving to university status the authors seek similarity and a direction of action for a Cypriot Higher Education College. Based on interviews and focus groups a proposed model for managing change in educational institutions undergoing this transition is offered.
Key features of appraisal effectiveness
Authors: Piggot‐Irvine Eileen
Published: June 2003

Provides an overview of performance management and appraisal in New Zealand schools. Outlines a model of principal appraisal that demonstrates an integration of development and accountability elements. Draws on three studies to develop a series of conclusions about the key features of appraisal effectiveness. Significant features are associated with relationships based on high trust and openness which, in turn, can lead to problem resolution and improved performance. An outline of how training can be targeted at helping appraisers to establish such relationships is provided. Other key features of effectiveness associated with objectivity, clarity and depth in objective setting are also discussed.
A comparison of different regularization methods for a Cauchy problem in anisotropic heat conduction
Authors: Mera N.S. , Elliott L. , Ingham D.B. , Lesnic D.
Published: June 2003

In this paper, various regularization methods are numerically implemented using the boundary element method (BEM) in order to solve the Cauchy steady‐state heat conduction problem in an anisotropic medium. The convergence and the stability of the numerical methods are investigated and compared. The numerical results obtained confirm that stable numerical results can be obtained by various regularization methods, but if high accuracy is required for the temperature, or if the heat flux is also required, then care must be taken when choosing the regularization method since the numerical results are substantially improved by choosing the appropriate method.
BEM/FVM conjugate heat transfer analysis of a three‐dimensional film cooled turbine blade
Authors: Kassab A. , Divo E. , Heidmann J. , Steinthorsson E. , Rodriguez F.
Published: June 2003

We report on the progress in the development and application of a coupled boundary element/finite volume method temperature‐forward/flux‐back algorithm developed to solve conjugate heat transfer arising in 3D film‐cooled turbine blades. We adopt a loosely coupled strategy where each set of field equations is solved to provide boundary conditions for the other. Iteration is carried out until interfacial continuity of temperature and heat flux is enforced. The NASA‐Glenn explicit finite volume Navier‐Stokes code Glenn‐HT is coupled to a 3D BEM steady‐state heat conduction solver. Results from a CHT simulation of a 3D film‐cooled blade section are compared with those obtained from the standard two temperature model, revealing that a significant difference in the level and distribution of metal temperatures is found between the two. Finally, current developments of an iterative strategy accommodating large numbers of unknowns by a domain decomposition approach is presented. An iterative scheme is developed along with a physically‐based initial guess and a coarse grid solution to provide a good starting point for the iteration. Results from a 3D simulation show the process that converges efficiently and offers substantial computational and storage savings.
A 3D surface offset method for STL‐format models
Authors: Qu Xiuzhi , Stucker Brent
Published: June 2003

This paper presents a new 3D offset method for modifying CAD model data in the STL format. In this method, vertices, instead of facets, are offset. The magnitude and direction of each vertex offset is calculated using the weighted sum of the normals of the facets that are connected to each vertex. To facilitate the vertex offset calculation, topological information is generated from the collection of unordered triangular facets making up the STL file. A straightforward algorithm is used to calculate the vertex offset using the adjoining facet normals, as identified from the topological information. This newly developed technique can successfully generate inward or outward offsets for STL models. As with any offset methodology, this technique has benefits and drawbacks, which will be discussed in this paper. Finally, conclusions will be made regarding the applicability of the developed methodology.
Biomaterial forming research using RP technology
Authors: Yan Yongnian , Wu Rendong , Zhang Renji , Xiong Zhuo , Lin Feng
Published: June 2003

This paper introduces a new subject called bio‐manufacturing. Bio‐manufacturing combines life science with manufacturing science, and uses manufacturing method to form materials with bio‐activity and bio‐degradability into scaffolds. In this paper, we discuss the hierarchy of bio‐manufacturing: the lower grade uses undegradable bio‐material to form permanent organ replacement such as auricular cartilage and the higher grade uses biodegradable bio‐materials to repair organ damage or organ replacement which degrades after embedded in the human body. They all adopt jetting/extrusion deposition process (fused deposition modelling or 3D printer), the distinct different point being the temperature of the forming chamber. The samples of bones and auricular cartilage produced by those processes had been practiced on dogs and rabbits, repaired their damage.
Stereo‐thermal‐lithography: a new principle for rapid prototyping
Authors: Bartolo P.J. , Mitchell G.
Published: June 2003

A new fabrication process for rapid prototyping is proposed in this paper. Optical and thermal effects are simultaneously used in this process to locally induce a phase change in a liquid resin. This phase change phenomena is used to “write” three‐dimensional shapes or patterns. Such objects or patterns can involve macroscopic engineering prototypes through to nanostructures for exploitation in waveguiding and photonic crystals. Several advantages can be achieved through this new process, in terms of accuracy, cost and time.
Improved surface finish in 3D printing using bimodal powder distribution
Authors: Lanzetta Michele , Sachs Emanuel
Published: June 2003

The use of bimodal powders has been shown to offer the possibility of dramatically improved surface finish in 3D printing. This work focused on individual lines, the primitive building block of 3D printed parts. It was observed that the fine component of bimodal ceramic powders, while uniformly distributed in the original powderbed, was preferentially found at the surface of the printed line, while the interior of the line was denuded of fines. Microscopic examination and approximate quantitative analysis supports the assertion that essentially all the fines have moved to the surface of the line. The mechanism for this rearrangement is not known, but is speculated to be related to the relative difficulty of wetting fine powders. The parameter space in which this phenomenon can be observed was examined in a preliminary manner.
The customized mandible substitute based on rapid prototyping
Authors: Yaxiong Liu , Dichen Li , Bingheng Lu , Sanhu He , Gang Li
Published: June 2003

Traditional standard bone substitutes cannot realize the individualized matching for the bones of different patients. In order to make a bone substitute match the shape of a patient's bone easily, a technology based on reverse engineering (RE) and rapid prototyping (RP) is put forward to design and fabricate a customized bone substitute. By RE, the customized bone substitute is designed according to the CT sectional pictures, and the customized localizer is designed to locate the customized bone substitute in the patient's body at the right position. A customized mandible substitute designed and fabricated by RE and RP has been put into clinical use and is discussed in detail. The results confirm that the advantage of RP in the field of bone restoration is that it can fabricate the customized bone substitute rapidly and accurately.