bluuebunny/crossref_metadata_2025 huggingface dataset:
Lipid Rafts in
Cryptococcus neoformans
Concentrate the Virulence Determinants Phospholipase B1 and Cu/Zn Superoxide Dismutase
Authors: Siafakas A. Rosemary , Wright Lesley C. , Sorrell Tania C. , Djordjevic Julianne T.
Published: March 2006

Lipid rafts have been identified in the membranes of mammalian cells, the yeast
Saccharomyces cerevisiae
, and the pathogenic fungus
Candida albicans
. Formed by a lateral association of sphingolipids and sterols, rafts concentrate proteins carrying a glycosylphosphatidylinositol (GPI) anchor. We report the isolation of membranes with the characteristics of rafts from the fungal pathogen
Cryptococcus neoformans
. These characteristics include insolubility in Triton X-100 (TX100) at 4°C, more-buoyant density within a sucrose gradient than the remaining membranes, and threefold enrichment with sterols. The virulence determinant phospholipase B1 (PLB1), a GPI-anchored protein, was highly concentrated in raft membranes and could be displaced from them by treatment with the sterol-sequestering agent methyl-β-cyclodextrin (MβCD). Phospholipase B enzyme activity was inhibited in the raft environment and increased 15-fold following disruption of rafts with TX100 at 37°C. Treatment of viable cryptococcal cells in suspension with MβCD also released PLB1 protein and enzyme activity, consistent with localization of PLB1 in plasma membrane rafts prior to secretion. The antioxidant virulence factor Cu/Zn superoxide dismutase (SOD1) was concentrated six- to ninefold in raft membrane fractions compared with nonraft membranes, whereas the cell wall-associated virulence factor laccase was not detected in membranes. We hypothesize that raft membranes function to cluster certain virulence factors at the cell surface to allow efficient access to enzyme substrate and/or to provide rapid release to the external environment.
Posttranslational, Translational, and Transcriptional Responses to Nitric Oxide Stress in
Cryptococcus neoformans
: Implications for Virulence
Authors: Missall Tricia A. , Pusateri Mary Ellen , Donlin Maureen J. , Chambers Kari T. , Corbett John A. , Lodge Jennifer K.
Published: March 2006

The ability of the fungal pathogen
Cryptococcus neoformans
to evade the mammalian innate immune response and cause disease is partially due to its ability to respond to and survive nitrosative stress. In this study, we use proteomic and genomic approaches to elucidate the response of
C. neoformans
to nitric oxide stress. This nitrosative stress response involves both transcriptional, translational, and posttranslational regulation. Proteomic and genomic analyses reveal changes in expression of stress response genes. In addition, genes involved in cell wall organization, respiration, signal transduction, transport, transcriptional control, and metabolism show altered expression under nitrosative conditions. Posttranslational modifications of transaldolase (Tal1), aconitase (Aco1), and the thiol peroxidase, Tsa1, are regulated during nitrosative stress. One stress-related protein up-regulated in the presence of nitric oxide stress is glutathione reductase (Glr1). To further investigate its functional role during nitrosative stress, a deletion mutant was generated. We show that this
glr1
Δ mutant is sensitive to nitrosative stress and macrophage killing in addition to being avirulent in mice. These studies define the response to nitrosative stress in this important fungal pathogen.
Differential Effects of Heterochromatin Protein 1 Isoforms on Mitotic Chromosome Distribution and Growth in
Dictyostelium discoideum
Authors: Kaller Markus , Euteneuer Ursula , Nellen Wolfgang
Published: March 2006

Heterochromatin protein 1 (HP1) is a well-characterized heterochromatin component conserved from fission yeast to humans. We identified three HP1-like genes (
hcpA
,
hcpB
, and
hcpC
) in the
Dictyostelium discoideum
genome. Two of these (
hcpA
and
hcpB
) are expressed, and the proteins colocalized as green fluorescent protein (GFP) fusion proteins in one major cluster at the nuclear periphery that was also characterized by histone H3 lysine 9 dimethylation, a histone modification so far not described for
Dictyostelium
. The data strongly suggest that this cluster represents the centromeres. Both single-knockout strains displayed only subtle phenotypes, suggesting that both isoforms have largely overlapping functions. In contrast, disruption of both isoforms appeared to be lethal. Furthermore, overexpression of a C-terminally truncated form of HcpA resulted in phenotypically distinct growth defects that were characterized by a strong decrease in cell viability. Although genetic evidence implies functional redundancy, overexpression of GFP-HcpA, but not GFP-HcpB, caused growth defects that were accompanied by an increase in the frequency of atypic anaphase bridges. Our data indicate that
Dictyostelium discoideum
cells are sensitive to changes in HcpA and HcpB protein levels and that the two isoforms display different in vivo and in vitro affinities for each other. Since the RNA interference (RNAi) machinery is frequently involved in chromatin remodeling, we analyzed if knockouts of RNAi components influenced the localization of H3K9 dimethylation and HP1 isoforms in
Dictyostelium
. Interestingly, heterochromatin organization appeared to be independent of functional RNAi.
Pheromones Are Essential for Male Fertility and Sufficient To Direct Chemotropic Polarized Growth of Trichogynes during Mating in
Neurospora crassa
Authors: Kim Hyojeong , Borkovich Katherine A.
Published: March 2006

Neurospora crassa
is a self-sterile filamentous fungus with two mating types,
mat A
and
mat a
. Its mating involves chemotropic polarized growth of female-specific hyphae (trichogynes) toward male cells of the opposite mating type in a process involving pheromones and receptors.
mat A
cells express the
ccg-4
pheromone and the
pre-1
receptor, while
mat a
strains produce mRNA for the pheromone
mfa-1
and the
pre-2
receptor; MFA-1 and CCG-4 are the predicted ligands for PRE-1 and PRE-2, respectively. In this study, we generated Δ
ccg-4
and Δ
mfa-1
mutants and engineered a
mat a
strain to coexpress
ccg-4
and its receptor,
pre-2
. As males, Δ
ccg-4 mat A
and Δ
mfa-1 mat a
mutants were unable to attract
mat a
and
mat A
trichogynes, respectively, and consequently failed to initiate fruiting body (perithecial) development or produce meiotic spores (ascospores). In contrast, Δ
ccg-4 mat a
and Δ
mfa-1 mat A
mutants exhibited normal chemotropic attraction and male fertility. Δ
ccg-4
Δ
mfa-1
double mutants displayed defective chemotropism and male sterility in both mating types. Heterologous expression of
ccg-4
enabled
mat a
males to attract
mat a
trichogynes, although subsequent perithecial differentiation did not occur. Expression of
ccg-4
and
pre-2
in the same strain triggered self-stimulation, resulting in formation of barren perithecia with no ascospores. Our results indicate that CCG-4 and MFA-1 are required for mating-type-specific male fertility and that pheromones (and receptors) are initial determinants for sexual identity during mate recognition. Furthermore, a self-attraction signal can be transmitted within a strain that expresses a pheromone and its cognate receptor.
The Actin Gene
ACT1
Is Required for Phagocytosis, Motility, and Cell Separation of
Tetrahymena thermophila
Authors: Williams Norman E. , Tsao Che-Chia , Bowen Josephine , Hehman Gery L. , Williams Ruth J. , Frankel Joseph
Published: March 2006

A previously identified
Tetrahymena thermophila
actin gene (C. G. Cupples and R. E. Pearlman, Proc. Natl. Acad. Sci. USA
83:
5160-5164, 1986), here called
ACT1
, was disrupted by insertion of a
neo3
cassette. Cells in which all expressed copies of this gene were disrupted exhibited intermittent and extremely slow motility and severely curtailed phagocytic uptake. Transformation of these cells with inducible genetic constructs that contained a normal
ACT1
gene restored motility. Use of an epitope-tagged construct permitted visualization of Act1p in the isolated axonemes of these rescued cells. In
ACT1Δ
mutant cells, ultrastructural abnormalities of outer doublet microtubules were present in some of the axonemes. Nonetheless, these cells were still able to assemble cilia after deciliation. The nearly paralyzed
ACT1Δ
cells completed cleavage furrowing normally, but the presumptive daughter cells often failed to separate from one another and later became reintegrated. Clonal analysis revealed that the cell cycle length of the
ACT1Δ
cells was approximately double that of wild-type controls. Clones could nonetheless be maintained for up to 15 successive fissions, suggesting that the
ACT1
gene is not essential for cell viability or growth. Examination of the cell cortex with monoclonal antibodies revealed that whereas elongation of ciliary rows and formation of oral structures were normal, the ciliary rows of reintegrated daughter cells became laterally displaced and sometimes rejoined indiscriminately across the former division furrow. We conclude that Act1p is required in
Tetrahymena thermophila
primarily for normal ciliary motility and for phagocytosis and secondarily for the final separation of daughter cells.
Fe-Hydrogenase Maturases in the Hydrogenosomes of
Trichomonas vaginalis
Authors: Pütz Simone , Dolezal Pavel , Gelius-Dietrich Gabriel , Bohacova Lenka , Tachezy Jan , Henze Katrin
Published: March 2006

Assembly of active Fe-hydrogenase in the chloroplasts of the green alga
Chlamydomonas reinhardtii
requires auxiliary maturases, the
S
-adenosylmethionine-dependent enzymes HydG and HydE and the GTPase HydF. Genes encoding homologous maturases had been found in the genomes of all eubacteria that contain Fe-hydrogenase genes but not yet in any other eukaryote. By means of proteomic analysis, we identified a homologue of HydG in the hydrogenosomes, mitochondrion-related organelles that produce hydrogen under anaerobiosis by the activity of Fe-hydrogenase, in the pathogenic protist
Trichomonas vaginalis
. Genes encoding two other components of the Hyd system, HydE and HydF, were found in the
T. vaginalis
genome database. Overexpression of HydG, HydE, and HydF in trichomonads showed that all three proteins are specifically targeted to the hydrogenosomes, the site of Fe-hydrogenase maturation. The results of Neighbor-Net analyses of sequence similarities are consistent with a common eubacterial ancestor of HydG, HydE, and HydF in
T. vaginalis
and
C. reinhardtii
, supporting a monophyletic origin of Fe-hydrogenase maturases in the two eukaryotes. Although Fe-hydrogenases exist in only a few eukaryotes, related Narf proteins with different cellular functions are widely distributed. Thus, we propose that the acquisition of Fe-hydrogenases, together with Hyd maturases, occurred once in eukaryotic evolution, followed by the appearance of Narf through gene duplication of the Fe-hydrogenase gene and subsequent loss of the Hyd proteins in eukaryotes in which Fe-hydrogenase function was lost.
Mutational Analysis of the Glycosylphosphatidylinositol (GPI) Anchor Pathway Demonstrates that GPI-Anchored Proteins Are Required for Cell Wall Biogenesis and Normal Hyphal Growth inNeurospora crassa
Authors: Bowman Shaun M. , Piwowar Amy , Al Dabbous Mash'el , Vierula John , Free Stephen J.
Published: March 2006

Using mutational and proteomic approaches, we have demonstrated the importance of the glycosylphosphatidylinositol (GPI) anchor pathway for cell wall synthesis and integrity and for the overall morphology of the filamentous fungusNeurospora crassa. Mutants affected in thegpig-1,gpip-1,gpip-2,gpip-3, andgpit-1genes, which encode components of theN. crassaGPI anchor biosynthetic pathway, have been characterized. GPI anchor mutants exhibit colonial morphologies, significantly reduced rates of growth, altered hyphal growth patterns, considerable cellular lysis, and an abnormal “cell-within-a-cell” phenotype. The mutants are deficient in the production of GPI-anchored proteins, verifying the requirement of each altered gene for the process of GPI-anchoring. The mutant cell walls are abnormally weak, contain reduced amounts of protein, and have an altered carbohydrate composition. The mutant cell walls lack a number of GPI-anchored proteins, putatively involved in cell wall biogenesis and remodeling. From these studies, we conclude that the GPI anchor pathway is critical for proper cell wall structure and function inN. crassa.
Single, Ancient Origin of a Plastid Metabolite Translocator Family in Plantae from an Endomembrane-Derived Ancestor
Authors: Weber Andreas P. M. , Linka Marc , Bhattacharya Debashish
Published: March 2006

Phylogenetic analyses show the single origin of a plastid metabolite translocator family in the Plantae from a gene encoding an existing endomembrane-derived protein. Red algal secondary endosymbiosis has spread a translocator gene into the ancestor of the “chromalveolate” protists, where it has diversified into a novel clade of proteins.
Structure-Function Relationships of Glucansucrase and Fructansucrase Enzymes from Lactic Acid Bacteria
Authors: van Hijum Sacha A. F. T. , Kralj Slavko , Ozimek Lukasz K. , Dijkhuizen Lubbert , van Geel-Schutten Ineke G. H.
Published: March 2006

Lactic acid bacteria (LAB) employ sucrase-type enzymes to convert sucrose into homopolysaccharides consisting of either glucosyl units (glucans) or fructosyl units (fructans). The enzymes involved are labeled glucansucrases (GS) and fructansucrases (FS), respectively. The available molecular, biochemical, and structural information on sucrase genes and enzymes from various LAB and their fructan and α-glucan products is reviewed. The GS and FS enzymes are both glycoside hydrolase enzymes that act on the same substrate (sucrose) and catalyze (retaining) transglycosylation reactions that result in polysaccharide formation, but they possess completely different protein structures. GS enzymes (family GH70) are large multidomain proteins that occur exclusively in LAB. Their catalytic domain displays clear secondary-structure similarity with α-amylase enzymes (family GH13), with a predicted permuted (β/α)
8
barrel structure for which detailed structural and mechanistic information is available. Emphasis now is on identification of residues and regions important for GS enzyme activity and product specificity (synthesis of α-glucans differing in glycosidic linkage type, degree and type of branching, glucan molecular mass, and solubility). FS enzymes (family GH68) occur in both gram-negative and gram-positive bacteria and synthesize β-fructan polymers with either β-(2→6) (inulin) or β-(2→1) (levan) glycosidic bonds. Recently, the first high-resolution three-dimensional structures have become available for FS (levansucrase) proteins, revealing a rare five-bladed β-propeller structure with a deep, negatively charged central pocket. Although these structures have provided detailed mechanistic insights, the structural features in FS enzymes dictating the synthesis of either β-(2→6) or β-(2→1) linkages, degree and type of branching, and fructan molecular mass remain to be identified.
The Where, When, and How of Organelle Acidification by the Yeast Vacuolar H
+
-ATPase
Authors: Kane Patricia M.
Published: March 2006

All eukaryotic cells contain multiple acidic organelles, and V-ATPases are central players in organelle acidification. Not only is the structure of V-ATPases highly conserved among eukaryotes, but there are also many regulatory mechanisms that are similar between fungi and higher eukaryotes. These mechanisms allow cells both to regulate the pHs of different compartments and to respond to changing extracellular conditions. The Saccharomyces cerevisiae V-ATPase has emerged as an important model for V-ATPase structure and function in all eukaryotic cells. This review discusses current knowledge of the structure, function, and regulation of the V-ATPase in S. cerevisiae and also examines the relationship between biosynthesis and transport of V-ATPase and compartment-specific regulation of acidification.
Sortases and the Art of Anchoring Proteins to the Envelopes of Gram-Positive Bacteria
Authors: Marraffini Luciano A. , DeDent Andrea C. , Schneewind Olaf
Published: March 2006

The cell wall envelopes of gram-positive bacteria represent a surface organelle that not only functions as a cytoskeletal element but also promotes interactions between bacteria and their environment. Cell wall peptidoglycan is covalently and noncovalently decorated with teichoic acids, polysaccharides, and proteins. The sum of these molecular decorations provides bacterial envelopes with species- and strain-specific properties that are ultimately responsible for bacterial virulence, interactions with host immune systems, and the development of disease symptoms or successful outcomes of infections. Surface proteins typically carry two topogenic sequences, i.e., N-terminal signal peptides and C-terminal sorting signals. Sortases catalyze a transpeptidation reaction by first cleaving a surface protein substrate at the cell wall sorting signal. The resulting acyl enzyme intermediates between sortases and their substrates are then resolved by the nucleophilic attack of amino groups, typically provided by the cell wall cross bridges of peptidoglycan precursors. The surface protein linked to peptidoglycan is then incorporated into the envelope and displayed on the microbial surface. This review focuses on the mechanisms of surface protein anchoring to the cell wall envelope by sortases and the role that these enzymes play in bacterial physiology and pathogenesis.
Adaptation and Acclimation of Photosynthetic Microorganisms to Permanently Cold Environments
Authors: Morgan-Kiss Rachael M. , Priscu John C. , Pocock Tessa , Gudynaite-Savitch Loreta , Huner Norman P. A.
Published: March 2006

Persistently cold environments constitute one of our world's largest ecosystems, and microorganisms dominate the biomass and metabolic activity in these extreme environments. The stress of low temperatures on life is exacerbated in organisms that rely on photoautrophic production of organic carbon and energy sources. Phototrophic organisms must coordinate temperature-independent reactions of light absorption and photochemistry with temperature-dependent processes of electron transport and utilization of energy sources through growth and metabolism. Despite this conundrum, phototrophic microorganisms thrive in all cold ecosystems described and (together with chemoautrophs) provide the base of autotrophic production in low-temperature food webs. Psychrophilic (organisms with a requirement for low growth temperatures) and psychrotolerant (organisms tolerant of low growth temperatures) photoautotrophs rely on low-temperature acclimative and adaptive strategies that have been described for other low-temperature-adapted heterotrophic organisms, such as cold-active proteins and maintenance of membrane fluidity. In addition, photoautrophic organisms possess other strategies to balance the absorption of light and the transduction of light energy to stored chemical energy products (NADPH and ATP) with downstream consumption of photosynthetically derived energy products at low temperatures. Lastly, differential adaptive and acclimative mechanisms exist in phototrophic microorganisms residing in low-temperature environments that are exposed to constant low-light environments versus high-light- and high-UV-exposed phototrophic assemblages.
The BAR Domain Proteins: Molding Membranes in Fission, Fusion, and Phagy
Authors: Ren Gang , Vajjhala Parimala , Lee Janet S. , Winsor Barbara , Munn Alan L.
Published: March 2006

The Bin1/amphiphysin/Rvs167 (BAR) domain proteins are a ubiquitous protein family. Genes encoding members of this family have not yet been found in the genomes of prokaryotes, but within eukaryotes, BAR domain proteins are found universally from unicellular eukaryotes such as yeast through to plants, insects, and vertebrates. BAR domain proteins share an N-terminal BAR domain with a high propensity to adopt α-helical structure and engage in coiled-coil interactions with other proteins. BAR domain proteins are implicated in processes as fundamental and diverse as fission of synaptic vesicles, cell polarity, endocytosis, regulation of the actin cytoskeleton, transcriptional repression, cell-cell fusion, signal transduction, apoptosis, secretory vesicle fusion, excitation-contraction coupling, learning and memory, tissue differentiation, ion flux across membranes, and tumor suppression. What has been lacking is a molecular understanding of the role of the BAR domain protein in each process. The three-dimensional structure of the BAR domain has now been determined and valuable insight has been gained in understanding the interactions of BAR domains with membranes. The cellular roles of BAR domain proteins, characterized over the past decade in cells as distinct as yeasts, neurons, and myocytes, can now be understood in terms of a fundamental molecular function of all BAR domain proteins: to sense membrane curvature, to bind GTPases, and to mold a diversity of cellular membranes.
Prognostic value of tumour regression grading and depth of neoplastic infiltration within the perirectal fat after combined neoadjuvant chemo-radiotherapy and surgery for rectal cancer
Authors: Benzoni E , Intersimone D , Terrosu G , Bresadola V , Cojutti A , Cerato F , Avellini C
Published: March 2006

Objective:To evaluate histological variables correlated with pathological response to chemo-radiotherapy protocols for rectal cancer and with local recurrence and survival.

Methods:From 1994 to 2003, 58 patients with rectal cancer were enrolled in a non-randomised study based on standardised treatment with radiotherapy, 5-fluorouracil, and surgical resection, followed by histological examination, including tumour regression grading and depth of neoplastic infiltration within the perirectal fat. All patients were followed up. Mean (SD) length of follow up was 55.3 (28.1) months, range 5 to 108.

Results:No case was found with no regression (grade 0). Tumour regression was defined as grade 1 in 24.5% of cases, grade 2 in 58.5%, grade 3 in 7.5%, and grade 4 (complete regression) in 9.5%. Neoplastic infiltration of >4 mm within the perirectal fat was found in 25.6% of cases in grade 1, 55.8% in grade, 2.7% in grade 3, and 11.6% in grade 4. In 80% cases of pT4 depth of neoplastic infiltration within the perirectal fat was >4 mm (100% were pN+), and the same spread was also found in 53.4% of pT2 and 86.2% of pT3. Pathological response was associated with regression grade (p = 0.006) and depth of neoplastic infiltration within the perirectal fat (p = 0.04). Tumour regression grading was an independent variable for pT (p = 0.0002), pN status (p = 0.00004), pathological staging (p = 0.000001), and local recurrence (p = 0.003).

Conclusions:Involvement of the lateral resection margins correlates with a poor prognosis and indicates the likelihood of local recurrence of rectal cancer. Tumour regression grading and the depth of neoplastic infiltration within the perirectal fat are important prognostic factors that need to be evaluated routinely.
Ezrin—a useful factor in the prognosis of nephrotic syndrome in children: an immunohistochemical approach
Authors: Ostalska-Nowicka D , Zachwieja J , Nowicki M , Kaczmarek E , Siwinska A , Witt M
Published: March 2006

Background:Minimal change disease (MCD) and diffuse mesangial proliferation (DMP) are the most common pathomorphological forms of nephrotic syndrome glomerulopathies in children. The clinical course of DMP can be characterised by either DMP-sensitivity (DMP-S) or DMP-resistance (DMP-R) to steroids, resulting in an unfavourable course of the glomerulopathy. Although the clinical processes of DMP-S and DMP-R are initially identical, resistance to steroids may be foreseen by the immunohistochemical expression of cytoskeleton-associated proteins in podocytes.

Aims:To estimate the immunohistochemical expression of ezrin in children with MCD, DMP and focal segmental glomerulosclerosis (FSGS) and to evaluate its usefulness in predicting resistance to steroids.

Materials and methods:Renal biopsy specimens of patients with MCD (n = 15), DMP (n = 16) and FSGS (n = 6) were taken. The control tissue consisted of normal-appearing cortex taken from kidneys resected for localised neoplasms (n = 6). The indirect immunohistochemical protocol for the use of a monoclonal antibody directed against ezrin was used.

Results:The immunohistochemical expression of ezrin in cases progressively reduced from MCD to DMP-S to DMP-R to FSGS. Except for DMP-R and FSGS (p>0.05), the difference in ezrin expression in podocytes was significant.

Conclusion:Ezrin can be a potent marker of podocyte injury (podocytopathy) and may help in the histological qualification of MCD, DMP and FSGS. The increased permeability of the filtration barrier in steroid-resistant and proteinuric glomerulopathies may be a consequence of subcellular changes in podocyte-associated proteins following decreased expression of ezrin.
CIRCUITS, THE GROUPS OF RICHARD THOMPSON, AND coNP-COMPLETENESS
Authors: BIRGET JEAN-CAMILLE
Published: March 2006

We construct a finitely presented group with coNP-complete word problem, and a finitely generated simple group with coNP-complete word problem. These groups are represented as Thompson groups, hence as partial transformation groups of strings. The proof provides a simulation of combinational circuits by elements of the Thompson–Higman group G3,1.
NONCOMMUTATIVE GRÖBNER BASES FOR THE COMMUTATOR IDEAL
Authors: HERMILLER SUSAN , McCAMMOND JON
Published: March 2006

Let I denote the commutator ideal in the free associative algebra on m variables over an arbitrary field. In this article we prove there are exactly m! finite Gröbner bases for I, and uncountably many infinite Gröbner bases for I with respect to total division orderings. In addition, for m = 3 we give a complete description of its universal Gröbner basis.
THE MISSING LINK FOR ω-RATIONAL SETS, AUTOMATA, AND SEMIGROUPS
Authors: DUPARC JACQUES , RISS MARIANE
Published: March 2006

In 1997, following the works of Klaus W. Wagner on ω-regular sets, Olivier Carton and Dominique Perrin introduced the notions of chains and superchains for ω-semigroups. There is a clear correspondence between the algebraic representation of each of these operations and the automata-theoretical one. Unfortunately, chains and superchains do not suffice to describe the whole Wagner hierarchy. We introduce a third notion that completes the task undertaken by these two authors.
FROM THE $\mathcal{ZPC}$ STRUCTURE OF A REGULAR EXPRESSION TO ITS FOLLOW AUTOMATON
Authors: CHAMPARNAUD J.-M. , NICART F. , ZIADI D.
Published: March 2006

The follow automaton of a regular expression, recently introduced by Ilie and Yu, is a quotient of the position automaton. The aim of this paper is to present an efficient computation of this quotient, based on specific properties of the [Formula: see text] structure of the expression.
NILPOTENT LINEAR SEMIGROUPS
Authors: JESPERS ERIC , RILEY DAVID
Published: March 2006

We characterize the structure of linear semigroups satisfying certain global and local nilpotence conditions and deduce various Engel-type results. For example, using a form of Zel'manov's solution of the restricted Burnside problem we are able to show that a finitely generated residually finite group is nilpotent if and only if it satisfies a certain 4-generator property of semigroups we call WMN. Methods of linear semigroups then allow us to prove that a linear semigroup is Mal'cev nilpotent precisely when it satisfies WMN. As an application, we show that a finitely generated associative algebra is nilpotent when viewed as a Lie algebra if and only if its adjoint semigroup is WMN.
SOME REMARKS ON ONE-RELATOR AMALGAMATED FREE PRODUCTS II
Authors: JUHÁSZ ARYE
Published: March 2006

We consider quotients of the free product G of groups A and B, amalgamated along a group C, which is malnormal in A and in B. We concentrate on quotients H of G by the normal closure of a single relator which is a power of a word. We show that a part of the results which are true for the corresponding one relator free products hold true for H. We reduce the problems to the free product case and use small cancellation theory.
GENERALIZED SINGULAR VALUE DECOMPOSITION AND ITS APPLICATIONS IN MODEL ANALYSIS
Authors: DULOV EUGENE V. , ZAPATA HUMBERTO SARRIA , ANDRIANOVA NATALIA A.
Published: March 2006

For a variety of processes we can observe and register their characteristics, making up a sequence of measurement vectors or matrices (rectangular in general). Our goal is to extract some model dependent information using the available information. Such approaches are typical in technology (for a neat chemistry example, see [7,9]) and model analysis like parameter identification of linear stochastic dynamic systems. Since a stochastic nature of financial and economic data is evident, we can extend this data analysis technique to a number of new applications.

If we are successful, some kind of adaptive filter can be further constructed (similar to the classic Kalman's one, for example). Inspired with formal model parameters, we can apply this filter to process financial data like stock information to predict and verify how close is a mathematical model to a real-time data.

Namely, when provided with a set measurements represented by matrices Ai∈ Mm,n(ℝ), we have to estimate a problem dependent characteristic matrices [Formula: see text] with P,Q being orthonormal matrices, Bi∈ Mr(ℝ), r ≤ min {m,n}. Formulated as above, the problem is usually called a generalized singular value decomposition (GSVD) problem and could be solved numerically [1, 2]. These matrices provide some basic information applicable for higher level automated problem solver or human interpretation.
TECHNICAL ANALYSIS BASED ON PRICE-VOLUME SIGNALS AND THE POWER OF TRADING BREAKS
Authors: WESTERHOFF FRANK H.
Published: March 2006

We propose a novel stock market model and investigate the effectiveness of trading breaks. Our nonlinear model consists of two types of traders: while fundamentalists expect prices to return towards their intrinsic values, chartists extrapolate past price movements into the future. Moreover, chartists condition their orders on past trading volume. The model is able to replicate several stylized facts of stock markets such as fat tails and volatility clustering. Using the model as an artificial stock market laboratory we find that trading breaks have the power to reduce volatility and — if fundamentals do not move too strongly — also mispricing.
PRICING DERIVATIVES ON TWO-DIMENSIONAL LÉVY PROCESSES
Authors: FAJARDO JOSÉ , MORDECKI ERNESTO
Published: March 2006

The aim of this work is to use a duality approach to study the pricing of derivatives depending on two stocks driven by a bidimensional Lévy process. The main idea is to apply Girsanov's Theorem for Lévy processes, in order to reduce the posed problem to a problem with one Lévy driven stock in an auxiliary market, baptized as "dual market". In this way, we extend the results obtained by Gerber and Shiu [5] for two-dimensional Brownian motion.
DOES THE APPLICATION OF INNOVATIVE INTERNAL MODELS DIMINISH REGULATORY CAPITAL?
Authors: KALYVAS LAMPROS , SFETSOS ATHANASIOS
Published: March 2006

The broad spectrum and the increased complexity of financial products that compose modern portfolios have forced credit and financial institutions to focus on innovative and more effective ways of estimating market risks. These new approaches, very often, prove to be more conservative compared to traditional approaches in terms of market risk quantification. On the other hand, according to the Basel Committee evaluation framework, this conservatism is rewarded with lower multiplication factors when calculations of capital requirements take place. The present study elaborates on the comparison of several Value-at-Risk (VaR) methodologies based on the capital requirements they provide according to the Basel Committee regulatory framework.
ALGORITHM FOR MODEL STUDY OF OFF-LATTICE PROTEIN FOLDING
Authors: LÜ ZHIPENG , HUANG WENQI
Published: March 2006

A three-dimensional AB off-lattice protein model, which involves two species of residues interacting through simplified backbone and modified Lennard-Jones potentials, is studied. Incorporating an extra energy contribution into the original potential energy function, we develop and study a simple gradient algorithm for finding the lowest energy states of this protein model. The performance of our algorithm is tested on the Fibonacci sequences of lengths ranging from 13 to 55 residues previously studied by Hsu et al. Computational performance and behavior of our algorithm are also discussed.
THE FORMATION AND DETECTION OF TIGHT-TURN IN PYRIMIDINE/PURINE/PYRIMIDINE TYPE DNA TRIPLEXES — NEW FINDINGS ON MOTIFS CC AND TT BY FLUORESCENCE SPECTROSCOPY AT pH 7
Authors: WEY MING-TSAI , KAN LOU-SING
Published: March 2006

DNA triplexes with 'tight turns', i.e., sharp turns without any intervening bases, are studied by fluorescence resonance energy transfer process (FRET). The particular turning motifs under consideration are CC and TT imbedded in triplexes (5′- F -( TC )3( CT )3- D + 5′- AGAGAG ) and (5′- F -( CT )3( TC )3- D + 5′- GAGAGA ), where F and D are 6-fluorescein and 4-(4-dimethylaminophenylazo) benzoic acid, respectively. The association equilibrium constants of the above two triplexes ranged from 1.7 × 107 to 2.9 × 104 and 0.75 × 107 to 1.8 × 104 from 10 to 35°C, respectively. The thermodynamic parameters of these two triplexes are comparable (△ H : -46.0 vs. -45.0 Kcal/mol ; △ S : -129 vs -127 cal/mol K ; △ G : -7.5 vs. -7.2 Kcal/mol , respectively). Thus, the stability of the tight-turn triplex with a CC motif is comparable to that with a TT motif, but slightly favored over the latter. This is the first report of a py/pu/py type triplex containing such tight turns studied under pH at 7. The importance is manifested in their stabilities maintained under physiological neutral condition, as opposed to previous studies only obtainable in acidic conditions.
NEW 2-D GRAPHICAL REPRESENTATION OF DNA SEQUENCES
Authors: WANG JIASONG , WANG WEIQUN
Published: March 2006

In this paper we present a novel 2-D graphical representation of DNA sequences in the first quadrant Cartesian coordinate system. This representation has been mathematically proven to be a zero length of circuit, i.e., without any degeneracy. A practicable formula based upon an iterative comparison method has been developed to calculate the frequencies of nucleic acid bases ( A , T , G , and C ) from the starting point to any considered point. Furthermore, this new graphical representation, in comparison with our previously published method, may have a unique application in representing the universal genetic code.
Ecto-5′-nucleotidase (cd73)-dependent and -independent generation of adenosine participates in the mediation of tubuloglomerular feedback in vivo
Authors: Huang Dan Yang , Vallon Volker , Zimmermann Herbert , Koszalka Patricia , Schrader Jürgen , Osswald Hartmut
Published: March 2006

Tubuloglomerular feedback (TGF) describes a sequence of events linking salt concentrations in tubular fluid at the macula densa to the vascular tone of the afferent arteriole and thus to the glomerular filtration rate (GFR) of the same nephron. The signal transduction pathways of TGF remain incompletely understood, but both ATP release from macula densa cells and local formation of adenosine were suggested to be involved in the process. To test the role of extracellular formation of adenosine by ecto-5′-nucleotidase (cd73) in TGF, in regulation of GFR, and in tubular reabsorption, renal clearance and micropunture experiments were performed in cd73 wild-type (cd73+/+) and knockout mice (cd73−/−). The cd73−/− mice presented normal mean arterial blood pressure, but modestly lower whole kidney and single nephron GFR (SNGFR). Fractional reabsorption of Na+ and K+ up to the late proximal tubule, distal tubule, as well as urine were not significantly different between cd73−/− and cd73+/+ mice. Lack of cd73 resulted in a diminished TGF response, as indicated by smaller changes of stop-flow pressure in response to increasing loop of Henle perfusion from 0 to 25 nl/min, smaller differences in SNGFR determined from paired proximal and distal tubular collections, and by smaller fractional changes of distal SNGFR in response to adding 6 nl/min of artificial tubular fluid to free-flowing proximal tubules. The TGF response in cd73+/+ mice and the residual TGF response in cd73−/− mice were completely inhibited by adenosine A1-receptor blockade. The results suggest that extracellular formation of adenosine by ecto-5′-nucleotidase (cd73) is dispensable for normal fluid, Na+, or K+ reabsorption along the nephron, but contributes to the regulation of GFR. Adenosine generated by both ecto-5′-nucleotidase (cd73)-dependent and -independent mechanisms participates in the mediation of TGF in vivo.
Percutaneous Coronary Intervention in Patients with End-Stage Renal Disease
Authors: Bocksch Wolfgang , Fateh-Moghadam Suzanne , Mueller Eda , Huehns Sonja , Waigand Juergen , Dietz Rainer
Published: March 2006

Patients with end-stage renal disease (ESRD) represent a growing number of patients in the cardiac catheterization laboratories worldwide. This is a consequence of the growing absolute number of ESRD patients in developed countries, better noninvasive diagnostic tools, better catheterization facilities and last-but-not-least better education of referring physicians about the incidence and prognosis of coronary artery disease (CAD) for patients with ESRD. There is growing evidence of the positive impact of coronary revascularization on long-term outcome of these patients. ESRD patients have a high comorbidity and are therefore better candidates for the less invasive approach using percutaneous coronary intervention (PCI) rather than coronary artery bypass surgery (CABG). From the view of the interventional cardiologist, ESRD patients represent one of the most challenging patient cohort concerning technical challenges and potential risk of complication for the patient. Percutaneous coronary intervention (PCI) including debulking techniques and stent implantation is the current standard therapy for patients with symptomatic single-vessel disease (SVD) and the preferred therapy for most patients with focal, polyfocal or even diffuse multi-vessel disease (MVD). Coronary bypass surgery is reserved for a decreasing number of patients with mechanically untreatable coronary lesions and unprotected left main stem stenosis. The problem of restenosis and subsequent target lesion revascularization has been decreased to a minimum by the use of drug-eluting stents (DES), even though prospective randomized trials including ESRD patients are lacking. In case of acute coronary syndromes, the need for immediate coronary angiography and subsequent revascularization by means of PCI should be pointed out.
Atherosclerosis and Vascular Calcification in Chronic Renal Failure
Authors: Campean V. , Neureiter D. , Varga I. , Runk F. , Reiman A. , Garlichs C. , Achenbach S. , Nonnast-Daniel B. , Amann K.
Published: March 2006

Cardiovascular complications are a major clinical problem in patients with chronic kidney disease and end-stage renal failure; cardiac death accounts for approximately 40–50% of all deaths in these patients. Death from cardiovascular causes is up to 20 times more common in uremic patients than in the general population with the risk being even higher than in patients with diabetes mellitus. A high rate of myocardial infarction and excessive cardiac mortality have repeatedly been documented in patients with kidney disease and renal failure. Not only is the prevalence of myocardial infarction high, but also the case fatality rate is significantly higher in uremic patients with and without diabetes, respectively, compared to nonuremic patients. This is of particular interest since the prevalence of coronary atheroma in uremic patients was shown to be approximately 30% by autopsy and coronary angiography studies. Thus, coronary factors, i.e. atherosclerosis, and non-coronary factors may play an important role in the genesis of cardiac complications in the renal patient. In addition, renal failure recently has also be identified as a predictor of mortality in different stages of peripheral vascular disease. In particular, marked differences in the pathogenesis, morphology and course of atherosclerosis and arteriosclerosis under the conditions of renal failure have been documented. Among others increased plaque formation and particularly higher proportion and intensity of vascular calcification have been found in clinical and autopsy studies. In addition to the so-called classical or traditional risk factors, an important role for nonclassical risk factors such as microinflammation, hyperphosphatemia and oxidative stress has been documented in patients with renal failure and is discussed in detail.
Hypoalbuminemia in Renal Failure: Pathogenesis and Therapeutic Considerations
Authors: Haller C.
Published: March 2006

Hypoalbuminemia is common in patients with end-stage renal disease (ESRD). It is caused by a combination of a reduced synthesis and an increased degradation of albumin. The altered albumin homeostasis in ESRD patients is caused by a systemic inflammatory state which correlates closely with mortality. Hypoalbuminemia is a strong predictor of an adverse prognosis, but it is not a pathogenic factor in itself. In critically ill patients in intensive care units, the intravenous administration of human serum albumin generally does not improve prognosis. In contrast, in hypoalbuminemic dialysis patients with volume overload and a reduced effective arterial volume the administration of albumin is based on the pathophysiological concept of increasing intravascular oncotic pressure to transfer extravascular fluid into the intravascular compartment for ultrafiltration in order to mobilize edema fluid.
Angiotensin II in the Failing Heart
Authors: Schulz R. , Heusch G.
Published: March 2006

In the failing heart, the local angiotensin II concentration is increased, and the extent of cardiac angiotensin II release is related to the clinical signs of heart failure. The enzymes involved in myocardial generation of angiotensin II are the angiotensin-converting enzyme (ACE) and chymases. While myocardial angiotensin II is mainly generated by chymases in the human heart, ACE inhibitors nevertheless improve left ventricular (LV) function, attenuate LV remodelling and reduce mortality in heart failure patients. These beneficial actions of ACE inhibitors, however, relate to their beneficial effect on kinin metabolism. Angiotensin II type 1 receptor (AT1) antagonists also mediate part of their beneficial effects through increased bradykinin formation. However, in contrast to ACE inhibitors, AT1 receptor antagonists attenuate downstream signalling of angiotensin II-induced AT1 receptor activation, which increases the activity of existing proteins (e.g. NADPH oxidase) and the de novo synthesis of proteins (e.g. inducible nitric oxide synthase, tumor necrosis factor-α ) in cardiomyocytes. Given the multiple actions of AT1 receptor activation on cardiomyocyte and non-cardiomyocyte function in the presence of an increased myocardial AngII concentration, the reduction of cardiovascular mortality and rate of hospitalization following AT1 receptor blockade in heart failure patients not receiving ACE inhibitors is not surprising. Most importantly, the beneficial effects of AT1 receptor blockade are not only achieved when used as an alternative to ACE inhibition, but also when used on top of ACE inhibitors.
Optimized Heart Failure Therapy and Complete Anemia Correction on Left-Ventricular Hypertrophy in Nondiabetic and Diabetic Patients Undergoing Hemodialysis
Authors: Hampl Hannelore , Hennig Lars , Rosenberger Christian , Gogoll Lutz , Riedel Eberhard , Scherhag Armin
Published: March 2006

Background: According to new guidelines, diabetes mellitus per se can be considered as stage I chronic heart failure (CHF). Available evidence suggests that patients suffering from both diabetes mellitus and renal insufficiency have disproportionately high rates of left-ventricular hypertrophy (LVH). Methods: Optimized heart failure therapy, including β-blockers, ACE-inhibitors and AT II-type-1-receptor-blockers, was prescribed in combination with complete anemia correction using epoetin beta (target hemoglobin: 13.5 g/dl for women; 14.5 g/dl for men) to 230 patients (55% male) with ambulatory hemodialysis, including 60 patients (52% male) with diabetes. Echocardiographic follow-up examinations were performed over a mean period of 4.4 ± 1.2 years. Results: Mean hemoglobin levels at the study end significantly increased to target levels in the entire study population and in patients with diabetes (both p < 0.001). Compared with baseline, significant improvements were seen in hemodialysis patients – both without and with diabetes – in left-ventricular mass index (–28.8 g/m2 [p < 0.001] and 29.0 g/m2 [p < 0.005], respectively), left-ventricular ejection fraction (+7.0% [p < 0.001] and +8.3% [p < 0.01], respectively) and in NYHA class (–0.84 [p < 0.01] and –1.12 [p < 0.01], respectively). Similar to the results in the overall population, a highly significant reduction in LVH (p < 0.005) and significant improvements in LVEF (p < 0.01) and NYHA class (p < 0.01) were seen in the high-risk subgroup of diabetic patients. Conclusions: Patients undergoing hemodialysis, with or without concomitant diabetes, benefit considerably from optimized, multifactorial heart failure therapy combined with complete anemia correction.
Anemia Management in Chronic Heart Failure: Lessons Learnt from Chronic Kidney Disease
Authors: Besarab Anatole , Soman Sandeep
Published: March 2006

The importance of anemia in chronic kidney disease (CKD) has become increasingly well recognized over recent years, as have the benefits of treating anemic CKD patients with recombinant human erythropoietin (rHuEPO, epoetin). As well as reducing the need for blood transfusions and the complications associated with renal failure in CKD patients, rHuEPO treatment decreases patient morbidity and mortality, particularly as a result of cardiovascular disease. The strong correlation between anemia, renal failure and cardiac failure is one that has received much attention recently, with each factor recognized to cause the other to worsen in a ‘vicious cycle’. Recent studies have concentrated on the possible benefits of anemia treatment in patients with CHF. Currently available data suggest improvements in CHF symptoms, left ventricular ejection fraction (LVEF) and a reduction of hospitalizations associated with anemia correction through epoetin treatment. Available data from CKD patients suggest that anemia management should begin as early as possible, although the optimal target level for individual patients is as yet unclear. In addition to the currently available evidence, additional large, randomized, controlled studies are required to further define the morbidity/mortality benefits of epoetin treatment in CHF patients with anemia.