bluuebunny/crossref_metadata_2025 huggingface dataset:
Paleomagnetism of Carboniferous strata from the Stellarton Gap
Authors: Morris W A
Published: November 2002

Deposition of Carboniferous sediments within the Stellarton Graben of Nova Scotia was controlled by displacements on the bounding Hollow and Cobequid fault systems. Periods of both normal and transcurrent faulting have occurred on both faults. As a result, models for the development of the Stellarton Basin have included a pull-apart basin and a thermal subsidence basin. Paleomagnetic study of stratigraphic sequences from within the graben showed evidence for three separate periods of remanence acquisition (ST3  ST2  ST1). Ordering the acquisition sequence for these three magnetizations is mainly circumstantial, being based on the distribution of each remanence phase relative to stratigraphic position and deformation of the strata. The oldest magnetization ST3 is grossly divergent from previously reported Carboniferous results suggesting an early period of large-scale clockwise rotation. Magnetization ST2 has a similar pole position to many others from Maritime Carboniferous basins located within the Appalachian orogenic belt. The divergence of these poles from the cratonic poles is interpreted as indicating that these magnetizations were acquired at a time when the reference horizontal was different to the present horizontal. The third magnetization ST3 is identical to a large number of late-stage Carboniferous regional overprint magnetizations. In summary, the paleomagnetic evidence suggests that the Stellarton Basin was formed in an early (Westphalian B to C) pull-apart phase that was followed by a later thermal subsidence phase.
Geosaurus vignaudi n.sp. (Crocodyliformes: Thalattosuchia), first evidence of metriorhynchid crocodilians in the Late Jurassic (Tithonian) of central-east Mexico (State of Puebla)
Authors: Frey Eberhard , Buchy Marie-Céline , Stinnesbeck Wolfgang , López-Oliva José Guadalupe
Published: November 2002

Thalattosuchian crocodilians of the genus Geosaurus have mostly been recorded from the Jurassic of Europe. A single species was reported from Argentina. Here we describe a new species of Geosaurus vignaudi from the middle Tithonian La Pimienta Formation of State of Puebla, Mexico. Diagnostic for this species are the extremely low tooth count and a rostroventrally directed process at the rostral terminus of the mandible combined with a pair of horizontally directed rostral teeth. The skull of the holotype shows bite marks that probably caused the death of the animal.
Spatial analysis methods for forest genetic trials
Authors: Dutkowski Gregory W , Silva João Costa e , Gilmour Arthur R , Lopez Gustavo A
Published: November 2002

Spatial analysis, using separable autoregressive processes of residuals, is increasingly used in agricultural variety yield trial analysis. Interpretation of the sample variogram has become a tool for the detection of global trend and "extraneous" variation aligned with trial rows and columns. We applied this methodology to five selected forest genetic trials using an individual tree additive genetic model. We compared the base design model with post-blocking, a first-order autoregressive model of residuals (AR1), that model with an independent error term (AR1η), a combined base and autoregressive model, an autoregressive model only within replicates and an autoregressive model applied at the plot level. Post-blocking gave substantial improvements in log-likelihood over the base model, but the AR1η model was even better. The independent error term was necessary with the individual tree additive genetic model to avoid substantial positive bias in estimates of additive genetic variance in the AR1 model and blurred patterns of variation. With the combined model, the design effects were eliminated, or their significance was greatly reduced. Applying the AR1η model to individual trees was better than applying it at the plot level or applying it on a replicate-by-replicate basis. The relative improvements achieved in genetic response to selection did not exceed 6%. Examination of the spatial distribution of the residuals and the variogram of the residuals allowed the identification of the spatial patterns present. While additional significant terms could be fitted to model some of the spatial patterns and stationary variograms were attained in some instances, this resulted in only marginal increases in genetic gain. Use of a combined model is recommended to enable improved analysis of experimental data.
Interactions among Kalmia angustifolia, soil characteristics, and the growth and nutrition of black spruce seedlings in two boreal Newfoundland plantations of contrasting fertility
Authors: Yamasaki Stephen H , Fyles James W , Titus Brian D
Published: November 2002

To determine the nature of the negative influence of Kalmia angustifolia L. on black spruce (Picea mariana (Mill.) BSP) seedling growth and foliar nutrient concentrations, the effect of proximity to Kalmia on spruce seedlings was studied on two Kalmia-dominated sites of contrasting soil characteristics in central Newfoundland. Spruce seedlings and the soil at the base of their stems were sampled, and spruce leader length and foliar N and P concentration, as well as various physicochemical soil characteristics, were determined. Path analysis was used to determine the strength of direct and indirect relationships among variables hypothesized to be causally linked. Path diagrams were generated based on current knowledge of nutrient cycling in boreal ecosystems and mechanisms previously hypothesized to account for the influence of Kalmia on black spruce. On the wetter and richer site, proximity to Kalmia was associated with reduced spruce growth and humus extractable NH4-N, suggesting nutrient competition. On the drier and poorer site, results were consistent with a direct negative effect of Kalmia on the N nutrition of spruce. On both sites, we also found evidence for a direct effect of Kalmia on spruce growth that is consistent with allelopathic effects on spruce function.
Structure de sapinières aménagées et anciennes du massif des Laurentides (Québec) et diversité des plantes invasculaires
Authors: Desponts Mireille , Desrochers André , Bélanger Louis , Huot Jean
Published: November 2002

This study was undertaken to determine the contribution of old-growth and senescent forest stands regenerated through clear-cutting to the biodiversity of wet boreal fir stands in eastern Quebec because overmature stands are becoming scarce in that region. The study area was located in the Laurentian Mountains north of the city of Québec. The structure and composition of nonvascular plant communities (mosses, hepatica, lichens, and saprophytic fungi) of old-growth forests were compared with those of mature or senescent fir stands harvested 60 years ago. Nonvascular plants have a more uniform structure and a lower diversity in mature than in senescent or old-growth forests. A variety of specialized soil- and wood-inhabiting species and many rare species not observed in mature stands regenerated through clear-cutting are found in the latter. Structural diversity of senescent second-growth fir stands becomes similar to that of old-growth stand because of mortality within the overstory. These structural characteristics favour the development of diversified nonvascular plant communities, especially wood-inhabiting species found on slightly decomposed woody debris and soil-inhabiting species that colonize disturbed soils.[Journal translation]
Dynamics of coarse woody debris following gap harvesting in the Acadian forest of central Maine, U.S.A.
Authors: Fraver Shawn , Wagner Robert G , Day Michael
Published: November 2002

We examined the dynamics of down coarse woody debris (CWD) under an expanding-gap harvesting system in the Acadian forest of Maine. Gap harvesting treatments included 20% basal area removal, 10% basal area removal, and a control. We compared volume, biomass, diameter-class, and decay-class distributions of CWD in permanent plots before and 3 years after harvest. We also determined wood density and moisture content by species and decay class. Mean pre-harvest CWD volume was 108.9 m3/ha, and biomass was 23.22 Mg/ha. Both harvesting treatments increased the volume and biomass of non-decayed, small-diameter CWD (i.e., logging slash), with the 20% treatment showing a greater increase than the 10% treatment and both treatments showing greater increases than the control. Post-harvest reduction of advanced-decay CWD due to mechanical crushing was not evident. A mean of 18.48 m3 water/ha (1.85 L/m2) demonstrates substantial water storage in CWD, even during an exceptionally dry sampling period. The U-shaped temporal trend in CWD volume or biomass seen in even-aged stands may not apply to these uneven-aged stands; here, the trend is likely more complex because of the superimposition of small-scale natural disturbances and repeated silvicultural entries.
The response of boreal forest songbird communities to fire and post-fire harvesting
Authors: Morissette J L , Cobb T P , Brigham R M , James P C
Published: November 2002

Post-fire timber harvesting (salvage logging) is becoming more prevalent as logging companies try to recover some of the economic losses caused by fire. Because salvaging is a relatively new practice and because of the common perception that burned areas are of little value to wildlife, few guidelines exist for salvaging operations. We surveyed birds in unburned and burned stands of jack pine (Pinus banksiana Lamb.), mixedwood, and trembling aspen (Populus tremuloides Michx.) to characterize the post-fire bird community in commercially important forest types. The effects of salvage logging were examined in mixedwood and jack pine. Using fixed-radius point counts, a total of 1430 individuals representing 51 species were detected during this study. Community analysis revealed that burned forests supported a distinct species assemblage of songbirds relative to unburned forests and that salvage logging significantly altered this community. An examination of guild composition showed that resident species, canopy and cavity nesters, and insectivores were the least likely to be detected in salvaged areas. Species less sensitive to salvage logging tended to be habitat generalists, omnivores, and species that nest on the ground or in shrubs. We suggest alternative management strategies that may help reduce the impact of salvage logging on the boreal forest songbird community.
Rapid fine root disappearance in a pine woodland: a substantial carbon flux
Authors: Stevens Glen N , Jones Robert H , Mitchell Robert J
Published: November 2002

Fine root production and mortality are difficult to estimate accurately, because some fine roots die within days of being produced, and many apparently healthy roots disappear rapidly with no obvious period of senescence. Such root dynamics are difficult to analyze without very fine-scaled temporal observations. To capture the behavior of short-lived and rapidly disappearing roots, we sampled minirhizotron tubes weekly for 11 months in a Pinus palustris Mill. woodland. Fine root ([Formula: see text]2 mm diameter) length production and length mortality during this period were 1.57 ± 0.23 mm·cm2(mean ± SE) and 1.19 ± 0.17 mm·cm2, respectively. Depending on the type of estimate used, rapid disappearance accounted for between 21 and 37% of total fine root mortality. Rapidly disappearing roots had relatively short life-spans, a median of just 10.5 days. Monthly sampling of the same data set underestimated length production by 15%, overestimated median root life-span by 60%, and obscured causes of root loss. If short-lived roots are not accounted for, total net primary productivity in temperate forests may be underestimated by as much as 10%. We propose that belowground herbivory is the leading explanation for this rapid disappearance.
Ten-year decomposition in a loblolly pine forest
Authors: Binkley Dan
Published: November 2002

A litter sandwich approach was used to examine the loss of mass, acidity, and nutrients through 10 years of decomposition in a stand of loblolly pine (Pinus taeda L.). Each year, a new layer of 3-mm mesh fiberglass was placed on the annual accumulation of litterfall. Ten years of decomposition led to a loss of about 80% of the litter organic matter (giving a decomposition constant of 0.1655), which predicted a steady-state mass of the forest floor within 10% of the observed value. The pH (in 0.1 M KCl) showed little variation over time, ranging just from 3.2 to 3.5. The decline in titratable acidity appeared related primarily to the loss of organic matter rather than to any change in the acid characteristics of the material. Nitrogen loss was slow; the 10-year-old cohort of material contained 70% as much nitrogen as the original material. The loss of other nutrients was rapid, exceeding 80% loss by 6 years for phosphorus, potassium, calcium, and magnesium. The litter-sandwich method for examining decomposition is an easy, long-term approach that appeared to provide reasonable representation of the dynamics of unconfined forest floor materials. Future work should test this method for examining the decomposition effects of litter quality, nutrient supply, and environmental conditions.
An inexpensive portable freezer for in situ freezing in the field
Authors: Dubuc Yves , Dubuc Jean , Bigras Francine J
Published: November 2002

A portable freezer was developed to apply frost to branches of large trees to study their growth and recuperation after frost application under natural conditions. The freezer measures 37.5 × 63.5 × 31.5 cm and weighs approximately 3 kg. It consists of two compartments, a freezing compartment and a dry ice compartment. The portable freezer provides a ramp-and-soak freezing pattern using a programmable controller. The nonfreezing temperature plateaus can be set from 1 to 6°C and maintained for 0 to 12 h. The cooling and warming rates can be programmed from 1 to 12°C·h1. Test temperatures can be maintained for a period of time ranging from 0 to 12 h at set temperatures. Freezers were tested without samples under controlled conditions at ambient temperatures of 0, 5, 10, 5, 15, 20, and 25°C. Under these conditions, the cooling and warming rates showed a deviation of less than ±1°C·h1at a set rate of 2°C·h1. The freezer provides test temperatures as low as 38°C and 47°C at ambient temperatures of 20 and 10°C, respectively. Freezers were also tested under field conditions on attached branches in mature white spruce (Picea glauca (Moench) Voss) trees under hardening conditions.
Genetic variation in wood properties of interior spruce. I. Growth, latewood percentage, and wood density
Authors: Ivkovich Milosh , Namkoong Gene , Koshy Mathew
Published: November 2002

Quantitative genetic variation in growth, latewood percentage, and wood density was investigated for British Columbia's interior spruce (the common name for white spruce, Picea glauca (Moench) Voss; Engelmann spruce, Picea engelmanni Parry ex Engelm.; and their hybrids). The study included 160 half-sib families from the East Kootenay and Prince George regions. At the time of sampling, progeny tests for those two regions were 20 and 22 years old, respectively. Univariate and multivariate restricted maximum likelihood (REML) estimates of genetic parameters were obtained. Estimates of genetic variances and heritabilities differed greatly across planting sites for the examined traits, especially after transplantation between the regions. Significant negative genetic correlation between overall growth and wood density was found for the East Kootenay progenies, while negative but nonsignificant genetic correlation between these traits was found for the Prince George progenies. Generally, there was no significant decrease in heritability for ring width and latewood percentage in successive growth rings. A general age trend for genetic correlation between those traits was not apparent, except that the correlation remained negative during the observed period. Our results show that it is not possible to select certain families as superior based on 1-year results because of the family by growing season interactions. Nevertheless, genetic ageage correlations for cumulative increments were high, having a decreasing trend with increasing difference in age.
Genetic variation in wood properties of interior spruce. II. Tracheid characteristics
Authors: Ivkovich Milosh , Namkoong Gene , Koshy Mathew
Published: November 2002

In this study we investigated quantitative genetic variation in tracheid characteristics in two genetic tests of British Columbia's interior spruce (the common name for white spruce, Picea glauca (Moench) Voss; Engelmann spruce, Picea engelmanni Parry ex Engelm.; and their hybrids). The study included 88 half-sib families from the East Kootenay and Prince George regions. We have developed a technique for quantitative assessment of tracheid characteristics by measuring cross-sectional dimensions. We obtained cell size, wall thickness and their ratio in early-, transition-, and late-wood classes within a growth ring. Tracheid length and microfibril angle were measured in the transition wood. A number of tracheid characteristics showed significant genetic variation, but heritability, phenotypic, and genetic correlation estimates varied across test sites within and outside regions of origin of parental trees. Ring width was determined, both phenotypically and genetically, by the number of tracheids and to a lesser extent by the by their mean size. On average, rings with larger tracheids did not have significantly thicker walls. Wider rings had lower mean wall to tracheid size ratio. Faster growth did not result in shorter tracheids in the transition wood. Longer tracheids had lower micro fibril angle. There were no particular benefits from considering the anatomical component traits for breaking the negative genetic correlation between growth and wood density.
Disturbance regimes of hemlock-dominated old-growth forests in northern New York, U.S.A.
Authors: Ziegler Susy Svatek
Published: November 2002

Old-growth forests often have complex, uneven age structures reflecting both the long time elapsed since a major disturbance and the periodic formation of small canopy gaps. I established 12 plots of 0.1 ha in four areas of old growth to describe the stand-scale disturbance regime of forests dominated by eastern hemlock (Tsuga canadensis (L.) Carrière) in northern Adirondack Park, N.Y., U.S.A. I analyzed radial-increment patterns of cores from all canopy trees (398 trees in total) on each plot to determine the date of accession to canopy for each tree. Major growth releases indicated disturbance events that resulted in either gap origin (16% of events) or release from suppression (82% of events). The average decadal rate of disturbance for all plots and decades of the 130-year period from 1850 to 1979 is 4.85.4% of current exposed crown area. The average canopy-tree residence time is 184211 years. The stand-scale disturbance regimes in these Adirondack forests are similar to those of hemlockhardwood forests in Wisconsin, Michigan, Pennsylvania, and New York. These hemlock-dominated old-growth stands appear to be in quasi-equilibrium when viewed together over 13 decades.
Fluorescent pseudomonad population sizes baited from soils under pure birch, pure Douglas-fir, and mixed forest stands and their antagonism towardArmillaria ostoyaein vitro
Authors: DeLong R L , Lewis Kathy J , Simard Suzanne W , Gibson Susan
Published: November 2002

The relationship between forest stand composition in southern interior British Columbia and fluorescent pseudomonad bacteria populations was investigated using seedling bioassays. The objectives of this study were to (i) compare the relative population sizes of fluorescent pseudomonads baited from soils in pure paper birch (Betula papyrifera Marsh.), pure Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco), and mixed stands of the two species and (ii) determine if fluorescent pseudomonads from these soils have inhibitory effects against the root pathogen Armillaria ostoyae (Romagn.) Herink in vitro. Soil from birch stands supported four times more pseudomonads on seedling baits than soil from Douglas-fir stands, with the mixed stands intermediate. Soil from young stands yielded twice as many rhizosphere pseudomonads as soil from mature stands. Pseudomonad population size was positively correlated with percent cover and density of birch, and negatively correlated with basal area of Douglas-fir, percent cover of Douglas-fir, and carbon/nitrogen ratio of the soil. Greater than 50% of the fluorescent isolates reduced radial growth of A. ostoyae by more than 20% and greater than 90% reduced biomass of the fungus in dual culture tests. Cell-free bacterial culture filtrates added to the growth medium also reduced growth of A. ostoyae. This study provides evidence that paper birch provides a more favorable environment for fluorescent pseudomonads than Douglas-fir and suggests a mechanism by which paper birch can positively influence the susceptibility of managed forest stands to Armillaria root disease.
Comment  Economics of a nest-box program for the conservation of an endangered species: a re-appraisal
Authors: Lindenmayer D B , MacGregor C , Gibbons P
Published: November 2002

Spring et al. (D.A. Spring, M. Bevers, J.O.S. Kennedy, and D. Harley. 2001. Can. J. For. Res. 31: 19922003) recently published a paper on the economics of a nest-box program for the endangered arboreal marsupial, Leadbeater's possum (Gymnobelideus leadbeateri) in southeastern Australian forests. While their paper is a useful one, there are some important limitations of nest-box programs that need to be highlighted. In the case of Leadbeater's possum, we have undertaken extensive nest-box studies in Victoria mountain ash (Eucalyptus regnans F. Muell.) forests, where the vast majority of populations of the species now occur. Although large numbers of nest boxes have been deployed, very few have actually been occupied, which is a major problem since the effectiveness of any nest-box program will depend on patterns of use by the target species. Given very low levels of nest-box occupancy, harvesting regimes such as those that lead to on-site tree retention are needed to better conserve hollow-dependent species like Leadbeater's possum. Moreover, the need for nest boxes in the first place indicates that logging practices are presently not ecologically sustainable, and modified forestry practices need to be adopted.
Terpenoids in the wood of Scots pine and Norway spruce seedlings exposed to ozone at different nitrogen availability
Authors: Manninen A -M , Utriainen J , Holopainen T , Kainulainen P
Published: November 2002

Scots pine (Pinus sylvestris L.) and Norway spruce (Picea abies (L.) Karst.) seedlings were exposed to low-level ozone (O3) in an open-air exposure system for three or two growing seasons, respectively. Simultaneously, seedlings were supplied with nutrient solution containing either optimum (control) nitrogen (N), 70% of optimum N (low N availability), or 150% of optimum N (high N availability). Carbon-based secondary compounds, e.g., terpenes and resin acids, were analysed from the stemwood. α-Pinene, 3-carene, and limonene + β-phellandrene were the major terpenes in pine wood, whereas α-pinene, β-pinene, and limonene + β-phellandrene dominated in the spruce wood. Palustric + levopimaric and abietic acids were the major resin acids in the wood of both species. Ozone exposure did not cause any remarkable changes in the concentrations and proportional quantities of terpenes and resin acids in the wood of either tree species. Nitrogen availability did not affect the concentrations of carbon-based secondary compounds either, and the effects on proportional quantities were slight and ambiguous with respect to N supply. We conclude that realistically elevated levels of O3 do not have effects on concentrations of carbon-based secondary compounds of conifer wood and N availability might cause only slight changes in them. Therefore, our results do not directly support the carbonnutrient balance hypothesis.
Coarse woody debris in old Pinus sylvestris dominated forests along a geographic and human impact gradient in boreal Fennoscandia
Authors: Rouvinen S , Kuuluvainen T , Karjalainen L
Published: November 2002

Coarse woody debris (CWD) was studied in old Pinus sylvestris L. dominated forests in three geographic regions in the middle boreal vegetation zone: (i) in Häme in southwestern Finland, characterized by a long history of forest utilization, (ii) in Kuhmo in northeastern Finland, with a more recent history of forest utilization, and (iii) in the Vienansalo wilderness area in northwestern Russia, characterized by large areas of almost natural forest. Within the geographic regions the measured 0.2-ha plots were divided into three stand types according to the degree of human impact: (i) natural stands, (ii) selectively logged stands, and (iii) managed stands. The results showed that compared with natural forests, forest management has strongly reduced both the amount and diversity of CWD. The highest total CWD volumes were found in the natural stands in Häme (mean 67 m3·ha1) and Kuhmo (92 m3·ha1) and in the selective logged stands in Vienansalo (80 m3·ha1), while the lowest CWD volumes were found in the managed stands in Häme (7 m3·ha1) and Kuhmo (22 m3·ha1). The duration of forest utilization also plays a role, as forests with short management histories (Kuhmo region) still carried structural legacies from earlier more natural stages of the forest. In addition to lower total CWD volumes, managed stands also largely lacked certain dead wood characteristics, particularly large dead trees and standing dead trees with structural diversity characteristics (such as stem breakage, leaning stems, and fire scars) when compared with natural and selectively logged stands. The CWD characteristics of stands selectively logged in the past were often comparable with those of natural stands, suggesting that old selectively logged stands can be of high value from the nature conservation point of view.
Optimal sampling schemes based on the anticipated variance with lack of fit
Authors: Mandallaz D
Published: November 2002

This note presents an important improvement for optimal sampling schemes based on the anticipated variance. The anticipated variance is defined as the average of the design-based variance under a simple stochastic model in which the trees are assumed to be uniformly and independently distributed within a given number of so-called Poisson strata. We consider two-phase two-stage cluster sampling schemes in which costs and terrestrial second-phase sampling density can vary over domains. The estimation procedure is based on post-stratification with respect to so-called working strata that do not need to be identical with the Poisson strata, usually unknown, which induces a lack of fit. It is then possible to derive analytically the optimal sampling schemes. Data from the Swiss National Inventory illustrates the method.
A CHARACTERIZATION OF KNOTS IN A SPATIAL GRAPH II
Authors: NIKKUNI RYO , ONDA KAZUKO
Published: November 2002

We characterize the knot types in a spatial embedding of a graph which is obtained from the 5-cycle by duplicating each edge. It is characterized in terms of the second coefficients of the Conway polynomials and the third derivatives at 1 of the Jones polynomials of knots.
FINITE TYPE INVARIANTS OF LINKS WITH A FIXED LINKING MATRIX
Authors: APPLEBOIM ELI
Published: November 2002

In this paper we introduce two theories of finite type invariants for framed links with a fixed linking matrix. We show that these theories are different from, but related to, the theory of Vassiliev invariants of knots and links. We will take special note of the case of zero linking matrix. i.e., zero-framed algebraically split links. We also study the corresponding spaces of "chord diagrams".
ON PSEUDO-RIBBON SURFACE-LINKS
Authors: KAWAUCHI AKIO
Published: November 2002

We first introduce the null-homotopically peripheral quadratic function of a surface-link to obtain a lot of pseudo-ribbon, non-ribbon surface-links, generalizing a known property of the turned spun torus-knot of a non-trivial knot. Next, we study the torsion linking of a surface-link to show that the torsion linking of every pseudo-ribbon surface-link is the zero form, generalizing a known property of a ribbon surface-link. Further, we introduce and algebraically estimate the triple point cancelling number of a surface-link.
TOPOLOGICAL CLASSIFICATION OF GENERIC REAL RATIONAL FUNCTIONS
Authors: NATANZON SERGEI , SHAPIRO BORIS , VAINSHTEIN ALEK
Published: November 2002

To any real rational function with generic ramification points we assign a combinatorial object, called a garden, which consists of a weighted labeled directed planar chord diagram and of a set of weighted rooted trees each corresponding to a face of the diagram. We prove that any garden corresponds to a generic real rational function, and that equivalent functions have equivalent gardens.
A SELF-LINKING FORMULA FOR CURVES IN THE HEISENBERG SPACE
Authors: DINIZ MARCOS M.
Published: November 2002

The formula Lk = Wr + Tw, which expresses the linking number of two curves that bound a ribbon as a sum of two terms, has particularly interested biologists and was used to understand the DNA structure. The study of Legendrian curves in contact manifolds, and in particular in the Heisenberg space, is attached to some important problems in geometry, as the problem of classification of contact structures. In this work, we show the analogue formula for curves in the Heisenberg space, we relate the writhing number with the Thurston-Benequin invariant of a Legendrian curve and derive some results directly from this formula.
ALTERNATING POLYNOMIALS OF ALTERNATING LINKS
Authors: TEDFORD STEVEN J.
Published: November 2002

Given an s-component alternating link L with general Alexander polynomial Δ(x1, …, xs), the polynamial (1 - xi) Δ (x1, …, xs) is alternating for all i. That is, [Formula: see text] with (-1)∑ ij ci1 ⋯ is ≥ 0.
FEYNMAN DIAGRAMS VIA GRAPHICAL CALCULUS
Authors: FIORENZA DOMENICO , MURRI RICCARDO
Published: November 2002

We use Reshetikhin-Turaev graphical calculus to define Feynman diagrams and prove that asymptotic expansions of Gaussian integrals can be written as a sum over a suitable family of graphs. We discuss how different kinds of interactions give rise to different families of graphs. In particular, we show how symmetric and cyclic interactions lead to "ordinary" and "ribbon" graphs respectively. As an example, the 't Hooft-Kontsevich model for 2D quantum gravity is treated in some detail.
ON THE KINKINESS OF CLOSED BRAIDS
Authors: BOHR CHRISTIAN
Published: November 2002

In this note, we prove a lower bound for the positive kinkiness of a closed braid which we then use to derive an estimate for the positive kinkiness of a link in terms of its Seifert system. As an application, we show that certain pretzel knots cannot be unknotted using only positive crossing changes. We also describe a subgroup of infinite rank in the smooth knot concordance group of which no element has a strongly quasipositive representative.
e2eXpress: END-TO-END BIOINFORMATICS AND KNOWLEDGE MANAGEMENT SYSTEM FOR MICROARRAYS
Authors: ADAK SUDESHNA
Published: November 2002

The advent of high-density microarrays has made it possible for scientists to measure the expression levels of thousands of genes simultaneously. Understanding and interpreting the massive volumes of microarray data is necessary to unravel the molecular basis of diseases and will someday lead to medicines tailored for individual genetic profiles.

One of the main barriers to realizing the full potential of microarrays today is the need for specialized bioinformatics and knowledge management solutions required to mine the microarray data for biological information. After initial efforts at clustering expression data based on similarity, scientists have recognized the need to cross-reference and correlate experimental data with external data sources, to improve the quality of the biological conclusions that can be drawn.

This paper describes e2eXpress, such an end-to-end Bioinformatics and Knowledge Management System for Microarrays. e2eXpress incorporates basic data management and analysis tasks with novel approaches for mining various molecular biological databases to summarize information regarding coregulated gene clusters. In particular, this paper describes two new algorithms: (a) Text Mining for Gene Clusters: a statistical algorithm that is aimed at deriving biologically relevant information for gene clusters from the biomedical literature; (b) Pathway Scoring for Gene Clusters: a computational algorithm that is aimed at deriving pathway related information for gene clusters.

This paper describes the variety of statistical and computational algorithms that are required to mine the transcriptome in conjunction with extraneous data sources that can lead to real biological advances.
CAN MARKOV CHAIN MODELS MIMIC BIOLOGICAL REGULATION?
Authors: KIM SEUNGCHAN , LI HUAI , DOUGHERTY EDWARD R. , CAO NANWEI , CHEN YIDONG , BITTNER MICHAEL , SUH EDWARD B.
Published: November 2002

A fundamental question in biology is whether the network of interactions that regulate gene expression can be modeled by existing mathematical techniques. Studies of the ability to predict a gene's state based on the states of other genes suggest that it may be possible to abstract sufficient information to build models of the system that retain steady-state behavioral characteristics of the real system. This study tests this possibility by: (i) constructing a finite state homogeneous Markov chain model using a small set of interesting genes; (ii) estimating the model parameters based on the observed experimental data; (iii) exploring the dynamics of this small genetic regulatory network by analyzing its steady-state (long-run) behavior and comparing the resulting model behavior to the observed behavior of the original system. The data used in this study are from a survey of melanoma where predictive relationships (coefficient of determination, CoD) between 587 genes from 31 samples were examined. Ten genes with strong interactive connectivity were chosen to formulate a finite state Markov chain on the basis of their role as drivers in the acquisition of an invasive phenotype in melanoma cells. Simulations with different perturbation probabilities and different iteration times were run. Following convergence of the chain to steady-state behavior, millions of samples of the results of further transitions were collected to estimate the steady-state distribution of network. In these samples, only a limited number of states possessed significant probability of occurrence. This behavior is nicely congruent with biological behavior, as cells appear to occupy only a negligible portion of the state space available to them. The model produced both some of the exact state vectors observed in the data, and also a number of state vectors that were near neighbors of the state vectors from the original data. By combining these similar states, a good representation of the observed states in the original data could be achieved. From this study, we find that, in this limited context, Markov chain simulation emulates well the dynamic behavior of a small regulatory network.
WHY MATHEMATICS IS NEEDED TO UNDERSTAND COMPLEX GENETICS DISEASES
Authors: KIMMEL MAREK
Published: November 2002

We discuss mathematical approaches to population genetics and evolutionary theory in the context of complex genetic disease. Mechanisms, which we discuss, include gene-environment interaction in lung cancer as well as classical mechanisms of stabilization of genetic disease such as overdominance, antagonistic pleiotropy and recurring mutations. Specific modeling approaches discussed include: (1) Mathematical model of the evolution of disease chromosome applied to mapping of a disease gene. (2) Iterated Galton–Watson branching process applied to modeling of trinucleotide expansion in triplet-repeat diseases. (3) Application of Ewens' sampling formula to analysis of Single Nucleotide Polymorphism haplotypes at disease-related genes. The aim of this paper is not to present an exhaustive review, but rather to advocate mathematical modeling approaches in a field of current interest.
ALTERED ABUNDANCE OF MESSENGER RNA TRANSCRIPTS WHOSE PRODUCTS HAVE MEMBRANE ATTACHMENT SITES IN PREGNANCY-INDUCED HYPERTENSION
Authors: SIMPSON GREGORY I. C. , SHARKEY LESLIE C. , FRAY JOHN
Published: November 2002

Pregnancy-induced hypertensive disorders (PIH) are leading causes of maternal mortality. Although the mechanism responsible for initiating and maintaining the disorder is unproven, physiologic molecular attachments in kidney and placenta play a role. The SHHF/Mcc-facp (SHHF) rat has features of the disorder, including abnormal placenta gene expression. To gain a molecular understanding of the gene expression profile associated with PIH, kidneys and placentas of SHHF rats at gestation day 20 were compared to WKY controls using microarray technology. We report that SHHF rats have spontaneous PIH, elevated total placenta weights, and reduced total pup weights than WKY controls and that they also have greater total number of mRNA transcripts expressed in placenta. Kidneys of SHHF rats, on the other hand, not only expressed disproportionately more predicted gene products with attachment sites such as RGD motifs, N-glycosylation sites, and N-myristoylation sites they also responded more profoundly to oral administration of L-arginine. We conclude that the increased abundance of transcripts whose products engage in posttranslational attachments using RGD motifs, N-glycosylation sites, and N-myristoylation sites and the reversal of these increases by oral administration of L-arginine suggests that NO may be of importance in PIH at the level of molecular attachments.
CONTROL OF STATIONARY BEHAVIOR IN PROBABILISTIC BOOLEAN NETWORKS BY MEANS OF STRUCTURAL INTERVENTION
Authors: SHMULEVICH ILYA , DOUGHERTY EDWARD R. , ZHANG WEI
Published: November 2002

Probabilistic Boolean Networks (PBNs) were recently introduced as models of gene regulatory networks. The dynamical behavior of PBNs, which are probabilistic generalizations of Boolean networks, can be studied using Markov chain theory. In particular, the steady-state or long-run behavior of PBNs may reflect the phenotype or functional state of the cell. Approaches to alter the steady-state behavior in a specific prescribed manner, in cases of aberrant cellular states, such as tumorigenesis, would be highly beneficial. This paper develops a methodology for altering the steady-state probabilities of certain states or sets of states with minimal modifications to the underlying rule-based structure. This approach is framed as an optimization problem that we propose to solve using genetic algorithms, which are well suited for capturing the underlying structure of PBNs and are able to locate the optimal solution in a highly efficient manner. Several computer simulation experiments support the proposed methodology.
RUNS OF AMINO ACIDS ARE LONGER THAN EXPECTED IN PROTEINS BASED ON A GRAPH THEORY REPRESENTATION OF THE GENETIC CODE
Authors: DIGBY DAVID , SEFFENS WILLIAM , ABEBE FISSEHA
Published: November 2002

An in silico study of mRNA secondary structure has found a bias within the coding sequences of genes that favors "in-frame" pairing of nucleotides. This pairing of codons, each with its reverse-complement, partitions the 20 amino acids into three subsets. The genetic code can therefore be represented by a three-component graph. The composition of proteins in terms of amino acid membership in the three subgroups has been measured, and sequence runs of members within the same subgroup have been analyzed using a runs statistic based on Z-scores. In a GENBANK database of over 416,000 protein sequences, the distribution of this runs-test statistic is negatively skewed. To assess whether this statistical bias was due to a chance grouping of the amino acids in the real genetic code, several alternate partitions of the genetic code were examined by permuting the assignment of amino acids to groups. A metric was constructed to define the difference, or "distance", between any two such partitions, and an exhaustive search was conducted among alternate partitions maximally distant from the natural partition of the genetic code, to select sets of partitions that were also maximally distant from one another. The statistical skewness of the runs statistic distribution for native protein sequences were significantly more negative under the natural partition than they were under all of the maximally different partition of codons, although for all partitions, including the natural one, the randomized sequences had quite similar skewness. Hence under the natural graph theory partition of the genetic code there is a preference for more protein sequences to contain fewer runs of amino acids, than they do under the other partitions, meaning that the average run must be longer under the natural partition. This suggests that a corresponding bias may exist in the coding sequences of the actual genes that code for these proteins.
COMPARISON OF DIFFERENT METHODOLOGIES TO IDENTIFY DIFFERENTIALLY EXPRESSED GENES IN TWO-SAMPLE cDNA MICROARRAYS
Authors: MARCHAL KATHLEEN , ENGELEN KRISTOF , DE BRABANTER JOS , AERTS STEIN , DE MOOR BART , AYOUBI TORIK , VAN HUMMELEN PAUL
Published: November 2002

This review compares different methods to identify differentially expressed genes in two-sample cDNA arrays. A two-sample experiment is a commonly used design to compare relative mRNA abundance between two different samples. This simple design is customarily used by biologists as a first screening before relying on more complex designs. Statistical techniques are quite well developed for such simple designs. For the identification of differentially expressed genes, four methods were described and compared: a fold test, a t-test (Long et al., 2001), SAM (Tusher et al., 2001) and an ANOVA-based bootstrap method (Kerr and Churchill, 2001). Mutual comparison of these methods clearly illustrates each method's advantages and pitfalls. Our analyses showed that the most reliable predictions are made by the combined use of different methods, each of which is based on a different statistic. The ANOVA-based bootstap method used in this study performed rather poorly in identifying differentially expressed genes.
INCONSISTENCIES BETWEEN MAPS OF HUMAN CHROMOSOME 22 CORRELATE WITH INCREASED FREQUENCY OF DISEASE-RELATED LOCI
Authors: CHELALA CLAUDE , DEVIGNES MARIE-DOMINIQUE , IMBEAUD SANDRINE , ZOOROB RIMA , AUFFRAY CHARLES , CURIS EMMANUEL , BÉNAZETH SIMONE , COX DAVID
Published: November 2002

The relationships between genetic or radiation hybrid (RH) and sequence maps of chromosome 22 have been reconsidered based on the sequence map. Integrated maps have been constructed by retaining only common markers between genetic or RH maps and the sequence map. Local inversions of markers have been detected. Ratios between either genetic or RH distances and sequence-based distances have been calculated for each map interval. Hot zones for recombination or radiation breakage have been delineated by merging together intervals displaying high distance ratios and located close to each other for sequence-constrained RH maps, and for female and male genetic maps. A statistically significant positive correlation was found between the distribution of disease-related genes and the hot zones for recombination or radiation breakage on both female genetic and Stanford-G3 RH maps. This observation indicates that investigation of chromosomal regions displaying inconsistencies between RH or genetic linkage and sequence-based maps can accelerate the initial phase of identification of disease-associated genes.
ANALYSIS OF THE EVOLVING PROTEOMES: PREDICTIONS OF THE NUMBER OF PROTEIN DOMAINS IN NATURE AND THE NUMBER OF GENES IN EUKARYOTIC ORGANISMS
Authors: KUZNETSOV VLADIMIR A. , PICKALOV VALERY V. , SENKO OLEG V. , KNOTT GARY D.
Published: November 2002

Motivation: Obtaining accurate estimates of the numbers of protein-coding genes and protein domains in a proteome, and the number of protein domains in nature is a daunting challenge. Computational analysis of the protein domain sets in the proteomes of many species allows us to estimate these numbers and to find their evolution relationships.

Results: We have analyzed the distributions of the number of occurrences of protein domains in sample proteomes of the 70 fully sequenced genome organisms of three major kingdoms of life: Archaea, Bacteria and Eukaryota. We found that a large fraction of the identified distinct protein domains (i.e., unique domains and homologous domain families) in these 70 proteomes (1051 (23%) out of 4493) are found in at least one organism in each of these kingdoms of life and that 43 (1%) of these domains are common to all the 70 organisms. All the observed domain occurrence frequency distributions for these 70 proteomes are well fitted by a family of Pareto-like functions, associated with the steady state distributions of a linear Markov random process. We present explicit formulas that accurately predict the number of distinct protein domains and the number of protein-coding genes for a given organism as functions of the number of non-redundant domain-to-protein links in the proteomes. These functions allows us to predict that there are 42,740, 27,900, and 21,200 protein-coding genes/open reading frames in the human, A. thaliana, and mouse genomes, respectively. We also estimate that there are 5271, 2955, and 4915 distinct protein domains in the human, A. thaliana, and mouse proteomes, respectively, and about 5500 distinct protein domains in the entire "proteome world".
FRACTIONAL INTEGRATION IN THE STOCK MARKET VOLATILITY SERIES
Authors: GIL-ALANA LUIS A.
Published: November 2002

In this article we model the stock market volatility in the US, the UK, France, Germany and Japan by means of using fractionally integrated techniques. The results, based on the tests of Robinson [24] show that the volatility series can be well described in terms of I(d) statistical processes, with d higher than 0.5 but smaller than 1, implying thus nonstationary but mean-reverting behaviour.
AMBIGUITY AND PORTFOLIO INERTIA
Authors: BASILI MARCELLO , FONTINI FULVIO
Published: November 2002

In this paper the Portfolio Choice problem is studied under ambiguity, formalized by means of the Choquet Expected Utility. Agents are supposed to be Choquet Expected Utility maximizers and are split into two categories: optimists, who hold a concave capacity, and pessimists, who hold a convex one. Portfolio inertia is defined and analyzed. Necessary and sufficient conditions are established between a specific structure of agents' beliefs, namely belief commonality, and Portfolio Inertia.
A PROCESS-RECONSTRUCTION ANALYSIS OF MARKET FLUCTUATIONS
Authors: VILELA MENDES R. , LIMA R. , ARAÚJO T.
Published: November 2002

The statistical properties of a stochastic process may be described (1) by the expectation values of the observables, (2) by the probability distribution functions or (3) by probability measures on path space. Here an analysis of level (3) is carried out for market fluctuation processes. Gibbs measures and chains with complete connections are considered. Some other topics are also discussed, in particular the asymptotic stationarity of the processes and the behavior of statistical indicators of level (1) and (2). We end up with some remarks concerning the nature and origin of the market fluctuation process and its relation to the efficient market hypothesis.