bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative analysis of 1st-year growth in six deciduous tree species
Authors: Farmer Jr. R. E.
Published: June 2008

Classical growth analysis was used to examine the basis of major variation in seedling growth characteristics among and within six deciduous tree species in nursery beds. A combination of high investment in leaf area and substantial net assimilation rate accounted for the high relative growth rate of Liriodendrontulipifera L. and Prunusserotina Ehrh.; these species also produced the largest seedlings in the test. Final weight of four Quercus species was closely associated with initial leaf area established at germination; Q. rubra L. and Q. prinus L. had the largest seedlings despite having net assimilation rates lower than Q. alba L. and Q. ilicifolia Wangenh., the smallest seedlings in the test. Within species, relative growth rate was significantly correlated with both net assimilation rate and relative growth rate of leaf area. Leaf area partition coefficient was positively correlated with relative growth rate in L. tulipifera, P. serotina, and Q. rubra but not in Q. alba, Q. prinus, and Q. ilicifolia.
A model of spread and intensification of dwarf mistletoe infection in young western hemlock stands
Authors: Bloomberg W. J. , Smith R. B. , Wereld A. Van Der
Published: June 2008

The following relationships were quantified in a mathematical computer model to predict spread and intensification of dwarf mistletoe (Arceuthobiumtsugense (Rosendahl) G. N. Jones) infection, originating from residual trees, in regeneration of western hemlock (Tsugaheterophylla (Raf.) Sarg.): distribution of dwarf mistletoe infections in residual source trees, dwarf mistletoe seed production, escape from crown and dispersal, interception of seeds by neighboring trees, distribution of seeds within crowns, development of dwarf mistletoe infections, mortality of plants, and tree crown growth. The model included options for thinning or sanitation by removal of infected residual or regeneration trees. Predictions by the model for a 10-year period did not differ significantly (p = 0.05) from results of a field plot with respect to average number of infections per tree, percentage of infections at 1-m distances from the residual tree, and percentage of infections in each quadrant centered on residual source tree. Predictions of the effects of stocking density and sanitation or thinning on infection agreed with results obtained from experiments with other tree species.
Use of diameter increment and basal area increment in tree growth studies
Authors: West P. W.
Published: June 2008

Growth of diameter of individual trees can be expressed as diameter increment or basal area increment. Little work has been done to determine which of these parameters is preferable for use in growth studies. This paper examines growth of trees in pure and mixed stands of even-aged, regrowth forest of Eucalyptusregnans, E. obliqua, and E. globulus, aged 6-80 years, thinned and unthinned, in southeastern Tasmania. Weighted least squares regression equations are developed to relate diameter and basal area increments, over 1- to 6-year increment periods, to initial tree diameter in 29 growth plots. The correlation between basal area increment and initial diameter was always greater than that between diameter increment and initial diameter in these relationships. Despite this, the precision of estimates of future diameter in each plot is shown to be the same whether diameter or basal area increment equations are used. Data from a thinning experiment in 38- to 85-year-old, even-aged Acersaccharum, Fraxinusamericana, and Prunusserotina stands in southern Ontario are also examined and similar results obtained. It is concluded that no apriori reason exists for expressing growth as diameter increment or basal area increment in studies of these types.
The potential of Weibull-type functions as flexible growth curves: discussion
Authors: Bailey Robert L.
Published: June 2008

not available
The impact of Hurricane David on the forests of Dominica
Authors: Lugo Ariel E. , Applefield Milton , Pool Douglas J. , McDonald Robert B.
Published: June 2008

The impact of Hurricane David on the forests of Dominica was measured 40 days after the hurricane struck the island on August 29, 1979, with winds averaging 92 km/h which lasted 10.2 h. Sixteen 0.1-ha plots were studied. They were located on a variety of slope and exposure conditions, representing three life zones and 11 plant associations. Measurements included tree diameter at breast height (dbh), total height, wood volume, and percent canopy closure of stand. Species and damage conditions were noted. The hurricane caused severe damage, particularly to forests on the southern half of the island. Forty-two percent of the standing timber volume in the study areas was damaged at an average intensity of 27 m3/ha. About 5.1 × I06 timber trees were damaged in an area of 246 km2. "Complex" vegetation was more resistant to hurricane damage than "simpler" vegetation. The climax Dacryodesexcelsa Vahl associations suffered the least hurricane damage, while the palm brake suffered the most damage. Only one species (Richeriagrandis Vahl) exhibited significantly higher hurricane damage. Trees in larger diameter classes tended to uproot with more frequency than smaller diameter trees, which tended to snap and break. Regrowth of seedlings and saplings was rapid on wet areas of the damaged sites. We found more species on regenerating plots than on the undisturbed forest plots. The damage caused by Hurricane David is the most extensive reported to date anywhere, and damage to vegetation by hurricanes appears to be more extensive than damage by earthquakes and landslides. Owing to their high frequencies in the Caribbean, hurricanes induce cyclic plant successions.
Growth, survival, and physiology of Douglas-fir seedlings following root wrenching and fertilization
Authors: Driessche R. van den
Published: June 2008

Douglas-fir (Pseudotsugamenziesii (Mirb.) Franco) seedlings were subjected to wrenching treatments during their 2nd year of growth in two experiments at different nurseries on Vancouver Island. Seedlings were wrenched with a fixed blade at 20–25 cm below the bed surface. In experiment 1 wrenching reduced water potential of trees on unirrigated loam soil by an average of 300 kPa during August and September. Wrenched trees lifted in October, which were stored at 2 °C until May, showed 25% higher survival than unwrenched trees 1 year after planting. Trees lifted in December had uniformly high survival (98%) and showed no effect of wrenching. Wrenched trees from irrigated plots had lower shoot length relative growth rates (RGR) than unwrenched trees during the year after planting. In experiment 2 wrenching treatments were applied to seedlings, growing in a loamy sand, for different periods between 15 May and 11 September as follows: (i) unwrenched, (ii) early summer, (iii) midsummer, (iv) late summer, (v) all summer. Three different levels of fertilization were applied to each wrenching treatment, and seedlings were lifted for storage at 2 °C in October and December. Stored trees and freshly lifted trees were planted at 700 m elevation on 3 March. Wrenching increased root dry weight, particularly when additional fertilizer was applied, but had no measurable effect on cold hardiness or root growth capacity. Nevertheless, late summer wrenching increased survival 5 and 7% above control 1 and 2 years after planting, when average survival was 47% after 1 year. Wrenching had little subsequent effect on new shoot growth of planted trees during 2 years after planting. However, late summer wrenched trees showed significantly more new shoot growth than all summer wrenched trees. Increasing fertilization reduced cold hardiness and survival of cold-stored trees, but increased root growth capacity. Cold hardiness, measured by electrical impedance, was correlated with survival of cold-stored trees after planting (r2 = 0.82). Root growth capacity, averaged over all fertilizer levels, was closely correlated with survival of stored and freshly lifted trees (r2 = 0.93). Foliar nutrient concentrations were reduced by wrenching, but fertilization increased nutrient reserves within the seedling.
Growth relationships in silver maple seedlings fumigated with O3 and SO2
Authors: Jensen K. F.
Published: June 2008

Growth analysis was used to measure the impact of low levels of ozone, alone and with sulfur dioxide, on the growth of silver maple (Acersaccharinum L.) seedlings. The seedlings were fumigated for up to 60 consecutive days with cither 0.05, 0.1, or 0.2 ppm ozone, alone and with 0.1 ppm SO2 for 12 h per day. Dry weight and leaf area development curves were calculated from data collected at 10-day intervals throughout the study. Growth analysis variables were calculated from these curves. Three variables, relative growth rate, relative leaf area growth rate, and relative leaf weight growth rate, were reduced by 0.2 ppm ozone and decreased even further when 0.1 ppm SO2 was applied. Neither the 0.05 nor 0.1 ppm ozone treatment decreased the relative growth rate of the silver maple seedlings. Even small differences in growth rate may produce large differences in dry matter accumulation over a growing season.
On the error of tree biomass tables constructed by a two-phase sampling design
Authors: Cunia T. , Michelakackis J.
Published: June 2008

It is common with forest biomass inventories to use one-way tree biomass tables (by diameter) constructed from (i) a two-way biomass table (by diameter and height) previously constructed for application to a large forest region, and (ii) a diameter–height relationship established from a sample of trees selected from the forest area being currently inventoried. A procedure is described to estimate the error of the one-way biomass table so constructed when the two-way biomass table and the diameter–height relationship are estimated by linear regression statistical techniques. The use of this procedure is then illustrated by applying it to a sample of 56 trees measured for biomass, diameter, and height and a sample of 224 trees measured for diameter and height alone.
Semiochemicals for the mountain pine beetle, Dendroctonusponderosae (Coleoptera: Scolytidae) in British Columbia: field trapping studies
Authors: Conn J. E. , Borden J. H. , Scott B. E. , Friskie L. M. , Pierce Jr. H. D. , Oehlschlager A. C.
Published: June 2008

The following compounds were field tested in multiple funnel or drainpipe traps as attractants for the mountain pine beetle, Dendroctonusponderosae Hopkins, in British Columbia lodgepole pine, Pinuscontorta var. latifolia Engelm. forests: trans-verbenol, 3-caren-10-ol, acetophenone, E-2-methyl-6-methylene-octa-2,7-dienol (myrcenol) and 2-p-menthen-7-ol (all female-produced volatiles which had proven attractive in laboratory bioassays); exo-brevicomin (produced by males); and α-pinene, β-pinene, 3-carene, β-phellandrene, terpinolene and myrcene (host tree monoterpenes). trans-Verbenol was demonstrated to be a highly active aggregation pheromone, as was (±)-exo-brevicomin. Myrcene was the most effective synergistic monoterpene, while α-pinene was completely ineffective. In one experiment, 3-caren-10-ol caused a shift in favor of responding males, but the other female-produced volatiles were inactive.
Semiochemicals for the mountain pine beetle, Dendroctonusponderosae (Coleoptera: Scolytidae), in British Columbia: baited-tree studies
Authors: Borden J. H. , Conn J. E. , Friskie L. M. , Scott B. E. , Chong L. J. , Pierce Jr. H. D. , Oehlschlager A. C.
Published: June 2008

Lodgepole pines, Pinuscontorta var. latifolia Engelm., in three interior British Columbia locations were baited with six monoterpenes alone or combined, and various combinations of the beetle-produced volatiles trans-verbenol, exo-brevicomin, and 3-caren-10-ol. Trees baited with trans-verbenol, exo brevicomin, and the monoterpene 3-carene sustained higher attack densities by the mountain pine beetle, Dendroctonusponderosae Hopkins, and were surrounded by more attacked trees than trees baited with trans-verbenol and 3-carene or unbaited controls. Myrcene was apparently the best of six monoterpenes as a synergist for trans-verbenol. 3-Caren-10-ol appeared to have some activity in an early test but did not prove to be an attractive pheromone in extensive studies. In a 17-ha portion of an infestation, treatment of 99 trees with 3-carene and trans-verbenol apparently caused a higher attack rate, resulting in 56.4% of the available green trees being attacked, as opposed to 22.3% of the available trees in the 14-ha unbaited area. These data as well as the high attack rates associated with trees which also had an exo-brevicomin bait suggest that semiochemicals could be used to contain D. ponderosae infestations and to attract beetles to lethal trap trees.
The effect of slash burning on the water repellency of forest soils at Vancouver, British Columbia
Authors: Henderson G. S. , Golding D. L.
Published: June 2008

Soil from 10 slash burned and 3 unburned clear-cuts was tested for water repellency by the water drop penetration method and compared with naturally occurring soil water repellency in uncut mature forest. There was no difference in soil water repellency between unburned clear-cuts and the uncut forest control. Soil was more frequently water repellent in slash burned sites (35% of samples) than in the control sites (21% of samples), but differences were significant only for the first 2 years after burning. All humus samples were severely water repellent. At the 0- to 4-cm depth below the humus, burned samples were more frequently repellent than control samples, but there was no difference at the 8- to 10-cm and 15+ cm depths. Water repellence decreased with depth in both burned and control sites.
A SURVEY ON SMALL FRAGMENTS OF FIRST-ORDER LOGIC OVER FINITE WORDS
Authors: DIEKERT VOLKER , GASTIN PAUL , KUFLEITNER MANFRED
Published: June 2008

We consider fragments of first-order logic over finite words. In particular, we deal with first-order logic with a restricted number of variables and with the lower levels of the alternation hierarchy. We use the algebraic approach to show decidability of expressibility within these fragments. As a byproduct, we survey several characterizations of the respective fragments. We give complete proofs for all characterizations and we provide all necessary background. Some of the proofs seem to be new and simpler than those which can be found elsewhere. We also give a proof of Simon's theorem on factorization forests restricted to aperiodic monoids because this is simpler and sufficient for our purpose.
FINE HIERARCHY OF REGULAR APERIODIC ω-LANGUAGES
Authors: SELIVANOV VICTOR
Published: June 2008

We develop a theory of regular aperiodic ω-languages in parallel with the theory around the Wagner hierarchy. In particular, we characterize the Wadge degrees of regular aperiodic ω-languages, find an effective version of the Wadge reducibility adequate for this class of languages and prove "aperiodic analogs" of the Büchi-Landweber determinacy theorem and of the Landweber's characterization of regular open and regular Gδ sets.
ON TRANSITION MINIMALITY OF BIDETERMINISTIC AUTOMATA
Authors: TAMM HELLIS
Published: June 2008

Bideterministic automata are deterministic automata with the property of their reversal automata also being deterministic. Bideterministic automata have previously been shown to be unique (up to an isomorphism) minimal NFAs with respect to the number of states. In this paper, we show that in addition to state minimality, bideterministic automata are also transition-minimal NFAs. However, as this transition minimality is not necessarily unique, we also present the necessary and sufficient conditions for a bideterministic automaton to be uniquely transition-minimal among NFAs. These results are obtained using the notion of the universal automaton. We also present some properties of the universal automaton. Furthermore, we show that bideterministic automata are transition-minimal ∊-NFAs.
ENERGY AND ANGULAR MOMENTUM OF GENERAL FOUR-DIMENSIONAL STATIONARY AXI-SYMMETRIC SPACE–TIME IN TELEPARALLEL GEOMETRY
Authors: NASHED GAMAL G. L.
Published: June 2008

We derive an exact general axi-symmetric solution of the coupled gravitational and electromagnetic fields in the tetrad theory of gravitation. The solution is characterized by four parameters: M (mass), Q (charge), a (rotation) and L (NUT). We then calculate the total exterior energy using the energy–momentum complex given by Møller in the framework of Weitzenböck geometry. We show that the energy contained in a sphere is shared by its interior as well as exterior. We also calculate the components of the spatial momentum to evaluate the angular momentum distribution. We show that the only nonvanishing components of the angular momentum is in the Z direction.
WHAT EINSTEIN DID NOT KNOW
Authors: PERL MARTIN L.
Published: June 2008

This public lecture is about 100 years of research on elementary particles and fundamental forces, beginning with the identification of the electron about 1900 and extending to the astonishing discovery of Dark Matter in the late 1900s. I talk about the elementary particle concept; the discoveries of leptons, quarks and force carrying particles; and some of the experimental technology used. I tell of my own research, our discovery of the tau lepton, our long, inconclusive search for fractional charged particles, and my new involvement in astronomical research on Dark Matter. I conclude by looking ahead to old unsolved puzzles and new questions on the fundamental nature of matter and force that face us in the 21st Century.
SEARCH FOR NEUTRAL BOSONS IN RELATIVISTIC HEAVY-ION COLLISIONS
Authors: JAIN P. L.
Published: June 2008

In this talk, I will describe results on 1,220 electron pairs produced from a 207 Pb beam at 160A GeV in a nuclear experiment EMU 11 conducted at the CERN SPS. These electron pairs were produced at a distance of more than 50 μm from the primary interactions, which eliminates contamination due to Dalitz pairs. Results on electron pairs with invariant mass Q ranging between 1 and 100 MeV and life-time τ between 10−15 s and 10−12 s were analyzed. After subtracting background pairs from the materialization of photons and from the decays of π0 to photons from the data, they exhibit an enhancement at low mass Q = 6 – 20 MeV with narrow peaks at 7 ± 1 MeV , 19 ± 1 MeV and τ ≤ 10−13 s .
PRECISION CALCULATIONS FOR FUTURE COLLIDERS
Authors: BAUR U.
Published: June 2008

I discuss the motivations for, and the status of, precision calculations for the Large Hadron Collider (LHC) and the planned International Linear Collider (ILC).
BREAKDOWN OF THE VACUUM BY A STRONG GRAVITATIONAL FIELD
Authors: MELISSINOS ADRIAN C.
Published: June 2008

Hawking radiation can be thought of as resulting from the breakdown of the vacuum into photon pairs due to the strong gravitational field at the bounding surface of black holes. We show how this argument can be made quantitative and obtain Hawking's result.
WINNING A BATTLE: THE IMPORTANCE OF KNOWING THE “NEIGHBORHOOD”
Authors: SHANAHAN LINDA , SEN SURAJIT
Published: June 2008

We propose that a battle between two conflicting entities can be modeled as a kinematic problem on a lattice. We examine the parameters relevant to such simulations, and describe global patterns emerging from a lattice model of a conflict with a few simple rules. We conclude that models of this type display interesting and relevant properties and warrant more in-depth analysis. The focus in this work is on the role of knowledge of the “neighborhood” in winning a battle.
An asymptotic approximation scheme for multigraph edge coloring
Authors: Sanders Peter , Steurer David
Published: June 2008

The edge coloring problem considers the assignment of colors from a minimum number of colors to edges of a graph such that no two edges with the same color are incident to the same node. We give polynomial time algorithms for approximate edge coloring of multigraphs, that is, parallel edges are allowed. The best previous algorithms achieve a fixed constant approximation factor plus a small additive offset. One of our algorithms achieves solution quality opt + √9opt/2 and has execution time polynomial in the number of nodes and the logarithm of the maximum edge multiplicity.
On the approximability of some network design problems
Authors: Chuzhoy Julia , Gupta Anupam , Naor Joseph (Seffi) , Sinha Amitabh
Published: June 2008

Consider the following classical network design problem: a set of terminals
T
= {

t
i

} wishes to send traffic to a root
r
in an
n
-node graph
G
= (
V
,
E
). Each terminal

t
i

sends

d
i

units of traffic and enough bandwidth has to be allocated on the edges to permit this. However, bandwidth on an edge
e
can only be allocated in
integral
multiples of some base capacity

u
e

and hence provisioning
k
×

u
e

bandwidth on edge
e
incurs a cost of ⌈k⌉ times the cost of that edge. The objective is a minimum-cost feasible solution.

This is one of many network design problems widely studied where the bandwidth allocation is governed by side constraints: edges can only allow a subset of cables to be purchased on them or certain quality-of-service requirements may have to be met.

In this work, we show that this problem and, in fact, several basic problems in this general network design framework cannot be approximated better than Ω(log log
n
) unless NP ⊆ DTIME (
n

O
(log log log
n
)

), where |
V
| =
n
. In particular, we show that this inapproximability threshold holds for (i) the Priority-Steiner Tree problem, (ii) the (single-sink) Cost-Distance problem, and (iii) the single-sink version of an even more fundamental problem, Fixed Charge Network Flow. Our results provide a further breakthrough in the understanding of the level of complexity of network design problems. These are the first nonconstant hardness results known for all these problems.
Efficient geographic routing over lossy links in wireless sensor networks
Authors: Zamalloa Marco Zúñiga , Seada Karim , Krishnamachari Bhaskar , Helmy Ahmed
Published: June 2008

Recent experimental studies have shown that wireless links in real sensor networks can be extremely unreliable, deviating to a large extent from the idealized perfect-reception-within-range models used in common network simulation tools. Previously proposed geographic routing protocols commonly employ a maximum-distance greedy forwarding technique that works well in ideal conditions. However, such a forwarding technique performs poorly in realistic conditions as it tends to forward packets on lossy links. Based on a recently developed link loss model, we study the performance of a wide array of forwarding strategies, via analysis, extensive simulations and a set of experiments on motes. We find that the product of the packet reception rate and the distance improvement towards destination (
PRR
×
d
) is a highly suitable metric for geographic forwarding in realistic environments.
Optimal sensor placement for agent localization
Authors: Jourdan Damien B. , Roy Nicholas
Published: June 2008

In this article we consider deploying a sensor network to help an agent navigate in an area. In particular the agent uses range measurements to the sensors to localize itself. We wish to place the sensors in order to provide optimal localization accuracy to the agent. We begin by considering the problem of placing sensors in order to optimally localize the agent at a
single
location. The Position Error Bound (PEB), a lower bound on the localization accuracy, is used to measure the quality of sensor configurations. We then present RELOCATE, an iterative algorithm that places the sensors so as to minimize the PEB at that point. When the range measurements are unbiased and have constant variances, we introduce a coordinate transform that allows us to obtain a closed-form solution to minimizing the PEB along one coordinate. We also prove that RELOCATE converges to the global minimum, and we compute the approximate expected rate of convergence of the algorithm. We then apply RELOCATE to the more complex case where the variance of the range measurements depends on the sensors location and where those measurements can be biased. We finally apply RELOCATE to the case where the PEB must be minimized not at a single point, but at
multiple
locations, so that good localization accuracy is ensured as the agent moves through the area. We show that, compared to Simulated Annealing, the algorithm yields better results faster on these more realistic scenarios. We also show that by optimally placing the sensors, significant savings in terms of number of sensors used can be achieved. Finally we illustrate that the PEB is not only a convenient theoretical lower bound, but that it can actually be closely approximated by a maximum likelihood estimator.
Partial network coding
Authors: Wang Dan , Zhang Qian , Liu Jiangchuan
Published: June 2008

Wireless sensor networks have been widely used for surveillance in harsh environments. In many such applications, the environmental data are continuously sensed, and data collection by a server is only performed occasionally. Hence, the sensor nodes have to temporarily store the data, and provide easy and on-hand access for the most updated data when the server approaches. Given the expensive server-to-sensor communications, the large amount of sensors and the limited storage space at each tiny sensor, continuous data collection becomes a challenging problem.

In this article, we present
partial network coding
(PNC) as a generic tool for these applications. PNC generalizes the existing
network coding
(NC) paradigm, an elegant solution for ubiquitous data distribution and collection. Yet PNC allows efficient storage replacement for continuous data, which is a deficiency of the conventional NC. We prove that the performance of PNC is quite close to NC, except for a sub-linear overhead on storage and communications. We then address a set of practical concerns toward PNC-based continuous data collection in sensor networks. Its feasibility and superiority are further demonstrated through simulation results.
Addressing thermal nonuniformity in SMT workloads
Authors: Winter Jonathan A. , Albonesi David H.
Published: June 2008

We explore DTM techniques within the context of uniform and nonuniform SMT workloads. While DVS is suitable for addressing workloads with uniformly high temperatures, for nonuniform workloads, performance loss occurs because of the slowdown of the cooler thread. To address this, we propose and evaluate DTM mechanisms that exploit the steering-based thread management mechanisms inherent in a clustered SMT architecture. We show that in contrast to DVS, which operates globally, our techniques are more effective at controlling temperature for nonuniform workloads. Furthermore, we devise a DTM technique that combines steering and DVS to achieve consistently good performance across all workloads.
In singulo Biochemistry: When Less Is More
Authors: Bustamante Carlos
Published: June 2008

It has been over one-and-a-half decades since methods of single-molecule detection and manipulation were first introduced in biochemical research. Since then, the application of these methods to an expanding variety of problems has grown at a vertiginous pace. While initially many of these experiments led more to confirmatory results than to new discoveries, today single-molecule methods are often the methods of choice to establish new mechanism-based results in biochemical research. Throughout this process, improvements in the sensitivity, versatility, and both spatial and temporal resolution of these techniques has occurred hand in hand with their applications. We discuss here some of the advantages of single-molecule methods over their bulk counterparts and argue that these advantages should help establish them as essential tools in the technical arsenal of the modern biochemist.
Moments of Discovery
Authors: Berg Paul
Published: June 2008

Devoted teachers and mentors during early childhood and adolescence nurtured my ambition to become a scientist, but it was not until I actually began doing experiments in college and graduate school that I was confident about that choice and of making it a reality. During my postdoctoral experiences and thereafter, I made several significant advances, most notably the discovery of the then novel acyl- and aminoacyl adenylates: the former as intermediates in fatty acyl coenzyme A (CoA) formation and the latter as precursors to aminoacyl tRNAs. In the early 1970s, my research changed from a focus on transcription and translation in Escherichia coli to the molecular genetics of mammalian cells. To that end, my laboratory developed a method for creating recombinant DNAs that led us and others, over the next two decades, to create increasingly sophisticated ways for introducing “foreign” DNAs into cultured mammalian cells and to target modifications of specific chromosomal loci. Circumstances surrounding that work drew me into the public policy debates regarding recombinant DNA practices. As an outgrowth of my commitment to teaching, I coauthored several textbooks on molecular genetics and a biography of George Beadle. The colleagues, students, and wealth of associates with whom I interacted have made being a scientist far richer than I can have imagined.
Eukaryotic DNA Ligases: Structural and Functional Insights
Authors: Ellenberger Tom , Tomkinson Alan E.
Published: June 2008

DNA ligases are required for DNA replication, repair, and recombination. In eukaryotes, there are three families of ATP-dependent DNA ligases. Members of the DNA ligase I and IV families are found in all eukaryotes, whereas DNA ligase III family members are restricted to vertebrates. These enzymes share a common catalytic region comprising a DNA-binding domain, a nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The catalytic region encircles nicked DNA with each of the domains contacting the DNA duplex. The unique segments adjacent to the catalytic region of eukaryotic DNA ligases are involved in specific protein-protein interactions with a growing number of DNA replication and repair proteins. These interactions determine the specific cellular functions of the DNA ligase isozymes. In mammals, defects in DNA ligation have been linked with an increased incidence of cancer and neurodegeneration.
Structure and Mechanics of Membrane Proteins
Authors: Engel Andreas , Gaub Hermann E.
Published: June 2008

Evolution has tuned membrane proteins to exist in a lipid bilayer, provide for cell-cell communication, transport solutes, and convert energies. These proteins exhibit a hydrophobic belt that interacts with the lipid bilayer. Detergents are therefore used to extract membrane proteins and keep them in solution for purification and subsequent analyses. However, most membrane proteins are unstable when solubilized and hence often not accessible to NMR or X-ray crystallography. The atomic force microscope (AFM) is a powerful tool for imaging and manipulating membrane proteins in their native state. Superb images of native membranes have been recorded, and a quantitative interpretation of the data acquired using the AFM tip has become possible. In addition, multifunctional probes to simultaneously acquire information on the topography and electrical properties of membrane proteins have been produced. This progress is discussed here and fosters expectations for future developments and applications of AFM and single-molecule force spectroscopy.
Translation at the Single-Molecule Level
Authors: Marshall R. Andrew , Aitken Colin Echeverría , Dorywalska Magdalena , Puglisi Joseph D.
Published: June 2008

Decades of studies have established translation as a multistep, multicomponent process that requires intricate communication to achieve high levels of speed, accuracy, and regulation. A crucial next step in understanding translation is to reveal the functional significance of the large-scale motions implied by static ribosome structures. This requires determining the trajectories, timescales, forces, and biochemical signals that underlie these dynamic conformational changes. Single-molecule methods have emerged as important tools for the characterization of motion in complex systems, including translation. In this review, we chronicle the key discoveries in this nascent field, which have demonstrated the power and promise of single-molecule techniques in the study of translation.
Response of a Warped Flexible Rotor with a Fluid Bearing
Authors: Meagher Jim , Wu Xi , Lencioni Chris
Published: June 2008

A two‐complex‐degrees‐of‐freedom model is developed and compared to
experimental data for various amounts of rotor bow and its orientation to mass imbalance
of the rotor. The equation of motion is developed by adding constant forces that rotate
with the rotor to a Bently‐Muszynska two‐mode isotropic rotor model with a plane journal
bearing. Diagnostic information discernable from probes at the bearing is explored and
compared to midspan response, where previous research has concentrated. The model
presented also extends earlier work by representing the effect of a nonrigid bearing. Good
agreement between the analytical model and experiment demonstrates that the analysis
presented can be useful to diagnose and balance residual shaft bow from probes
located at the bearings, where vibration data are typically more available than midspan probes.
Synergistic Effects of PPARγ Ligands and Retinoids in Cancer Treatment
Authors: Shimizu Masahito , Moriwaki Hisataka
Published: June 2008

Peroxisome proliferator‐activated receptors (PPARs) are members of the nuclear receptor superfamily. The activation of PPARs by their specific ligands is regarded as one of the promising strategies to inhibit cancer cell growth. However, recent clinical trials targeting several common cancers showed no beneficial effect when PPAR ligands are used as a monotherapy. Retinoid X receptors (RXRs), which play a critical role in normal cell proliferation as a master regulator for nuclear receptors, preferentially form heterodimers with PPARs. A malfunction of RXRα due to phosphorylation by the Ras/MAPK signaling pathway is associated with the development of certain types of human malignancies. The activation of PPARγ/RXR heterodimer by their respective ligands synergistically inhibits cell growth, while inducing apoptosis in human colon cancer cells when the phosphorylation of RXRα was inhibited. We here in review the synergistic antitumor effects produced by the combination of the PPAR, especially PPARγ, ligands plus other agents, especially retinoids, in a variety of human cancers. We also focus on the phosphorylation of RXRα because the inhibition of RXRα phosphorylation and the restoration of its physiological function may activate PPAR/RXR heterodimer and, therefore, be a potentially effective and critical strategy for the inhibition of cancer cell growth.
NO‐Donating NSAIDs, PPARδ, and Cancer: Does PPARδ Contribute to Colon Carcinogenesis?
Authors: Mackenzie Gerardo G. , Rasheed Shaheen , Wertheim William , Rigas Basil
Published: June 2008

The chemopreventive NO‐donating NSAIDs (NO‐NSAIDs; NSAIDs with an NO‐releasing moiety) modulate PPARδ and offer the opportunity to revisit the controversial role of PPARδ in carcinogenesis (several papers report that PPARδ either promotes or inhibits cancer). This review summarizes the pharmacology of NO‐NSAIDs, PPARδ cancer biology, and the relationship between the two. In particular, a study of the chemopreventive effect of two isomers of NO‐aspirin on intestinal neoplasia in Min mice showed that, compared to wild‐type controls, PPARδ is overexpressed in the intestinal mucosa of Min mice; PPARδ responds to
m‐ and p‐NO‐ASA proportionally to their antitumor effect (p‐ >m‐). This effect is accompanied by the induction of epithelial cell death, which correlates with the antineoplastic effect of NO‐aspirin; and NO‐aspirin′s effect on PPARδ is specific (no changes in PPARα or PPARγ). Although these data support the notion that PPARδ promotes intestinal carcinogenesis and its inhibition could be therapeutically useful, more work is needed before a firm conclusion is reached.
Pt(II) and Pd(II) Complexes with β‐Alanine
Authors: Krylova L. F. , Kovtunova L. M. , Romanenko G. V.
Published: June 2008

A sequence of stages in the syntheses of isomeric bisamino acid complexes of Pt(II) with β‐aminopropionic acid (β‐alanine = β‐AlaH) has been studied by the  195Pt NMR spectroscopy. The techniques have been developed of the synthesis of the cis‐ and trans‐bischelates of Pt(II) and Pd(II) with β‐alanine as well as of the halide complexes of trans‐[M(β‐AlaH) 2Cl2] (M = Pt, Pd) and trans‐K2[Pt(β‐Ala) 2I2] types. The NMR spectroscopy and IR spectroscopy (in the nuclei of  195Pt,  13C,  1H) and X‐ray diffraction analysis have been used to examine the structures of the synthesized compounds.
Estrogen Receptor-α and Endothelial Nitric Oxide Synthase Nuclear Complex Regulates Transcription of Human Telomerase
Authors: Grasselli Annalisa , Nanni Simona , Colussi Claudia , Aiello Aurora , Benvenuti Valentina , Ragone Gianluca , Moretti Fabiola , Sacchi Ada , Bacchetti Silvia , Gaetano Carlo , Capogrossi Maurizio C. , Pontecorvi Alfredo , Farsetti Antonella
Published: June 2008

We report that in endothelial cells, the angiogenic effect of 17β-estradiol (E2) is inhibited by the estrogen receptor (ER) antagonist ICI or the NO synthase (NOS) inhibitor 7-nitroindazole via downregulation of hTERT, the telomerase catalytic subunit, suggesting that E2 and NO are involved in controlling hTERT transcription. Quantitative Real-Time PCR and chromatin immunoprecipitations in E2-treated human umbilical vein endothelial cells, showed recruitment of ERs on the hTERT promoter and concomitant enrichment in histone 3 methylation at Lysine 79, a modification associated with transcription-competent chromatin. Confocal microscopy and re-chromatin immunoprecipitations revealed that on E2 induction, endothelial (e)NOS rapidly localized into the nucleus and associated with ERα on the hTERT promoter. Transfections of a constitutively active eNOS mutant (S1177D) strongly induced the hTERT promoter, indicating a direct role of the protein in hTERT transcriptional regulation. Mutation of the estrogen response element in the promoter abolished response to both ERs and active eNOS, demonstrating that the estrogen response element integrity is required for hTERT regulation by these factors. To investigate this novel regulation in a reduced NO environment, pulmonary endothelial cells were isolated from eNOS
−/−
mice and grown with/without E2. In wild-type cells, E2 significantly increased telomerase activity. In eNOS
−/−
cells, basal telomerase activity was rescued by exogenous eNOS or an NO donor, whereas responsiveness to E2 demanded the active protein. In conclusion, we document the novel findings of a combinatorial eNOS/ERα complex at the hTERT estrogen response element site and that active eNOS and ligand-activated ERs cooperate in regulating hTERT expression in the endothelium.
Myocardial Induction of Nucleostemin in Response to Postnatal Growth and Pathological Challenge
Authors: Siddiqi Sailay , Gude Natalie , Hosoda Toru , Muraski John , Rubio Marta , Emmanuel Gregory , Fransioli Jenna , Vitale Serena , Parolin Carola , D'Amario Domenico , Schaefer Erik , Kajstura Jan , Leri Annarosa , Anversa Piero , Sussman Mark A.
Published: June 2008

Stem cell–specific proteins and regulatory pathways that determine self-renewal and differentiation have become of fundamental importance in understanding regenerative and reparative processes in the myocardium. One such regulatory protein, named nucleostemin, has been studied in the context of stem cells and several cancer cell lines, where expression is associated with proliferation and maintenance of a primitive cellular phenotype. We find nucleostemin is present in young myocardium and is also induced following cardiomyopathic injury. Nucleostemin expression in cardiomyocytes is induced by fibroblast growth factor-2 and accumulates in response to Pim-1 kinase activity. Cardiac stem cells also express nucleostemin that is diminished in response to commitment to a differentiated phenotype. Overexpression of nucleostemin in cultured cardiac stem cells increases proliferation while preserving telomere length, providing a mechanistic basis for potential actions of nucleostemin in promotion of cell survival and proliferation as seen in other cell types.
Nitrite Anion Provides Potent Cytoprotective and Antiapoptotic Effects as Adjunctive Therapy to Reperfusion for Acute Myocardial Infarction
Authors: Gonzalez Felix M. , Shiva Sruti , Vincent Pamela S. , Ringwood Lorna A. , Hsu Li-Yueh , Hon Yuen Yi , Aletras Anthony H. , Cannon Richard O. , Gladwin Mark T. , Arai Andrew E.
Published: June 2008

Background—

Accumulating evidence suggests that the ubiquitous anion nitrite (NO
2
−
) is a physiological signaling molecule, with roles in intravascular endocrine nitric oxide transport, hypoxic vasodilation, signaling, and cytoprotection. Thus, nitrite could enhance the efficacy of reperfusion therapy for acute myocardial infarction. The specific aims of this study were (1) to assess the efficacy of nitrite in reducing necrosis and apoptosis in canine myocardial infarction and (2) to determine the relative role of nitrite versus chemical intermediates, such as
S
-nitrosothiols.

Methods and Results—

We evaluated infarct size, microvascular perfusion, and left ventricular function by histopathology, microspheres, and magnetic resonance imaging in 27 canines subjected to 120 minutes of coronary artery occlusion. This was a blinded, prospective study comparing a saline control group (n=9) with intravenous nitrite during the last 60 minutes of ischemia (n=9) and during the last 5 minutes of ischemia (n=9). In saline-treated control animals, 70±10% of the area at risk was infarcted compared with 23±5% in animals treated with a 60-minute nitrite infusion. Remarkably, a nitrite infusion in the last 5 minutes of ischemia also limited the extent of infarction (36±8% of area at risk). Nitrite improved microvascular perfusion, reduced apoptosis, and improved contractile function.
S
-Nitrosothiol and iron-nitrosyl-protein adducts did not accumulate in the 5-minute nitrite infusion, suggesting that nitrite is the bioactive intravascular nitric oxide species accounting for cardioprotection.

Conclusions—

Nitrite has significant potential as adjunctive therapy to enhance the efficacy of reperfusion therapy for acute myocardial infarction.
Diagnostic Errors in Pediatric Echocardiography
Authors: Benavidez Oscar J. , Gauvreau Kimberlee , Jenkins Kathy J. , Geva Tal
Published: June 2008

Background—

Despite increased interest in complications within pediatric cardiology, the domain of imaging-related diagnostic errors has received little attention. We developed a new taxonomy for diagnostic errors within pediatric echocardiography that categorizes errors by severity, preventability, and primary contributor. Our objectives were to examine its findings when applied to diagnostic error cases and to identify risk factors for preventable or possibly preventable diagnostic errors.

Methods and Results—

Diagnostic errors were identified at a high-volume academic pediatric cardiac center from December 2004 to August 2007. Demographic, clinical, and situational variables were collected from these cases and controls. During the study period, ≈50 660 echocardiograms were performed. Among the 87 diagnostic error cases identified, 70% affected clinical management or the patient was at risk of or experienced an adverse event. One third of the errors were preventable and 46% were possibly preventable; 69% of preventable errors were of moderate severity or greater. Univariate analysis demonstrated that preventable or possibly preventable errors were more likely to involve younger patients, lower body weight, study location, sedated/anesthetized patients, studies performed and interpreted at night, uncommon diagnoses, and greater anatomic complexity than controls. Multivariate analysis identified the following risk factors: rare or very rare diagnoses (adjusted odds ratio [AOR], 9.2;
P
<0.001), study location in the recovery room (AOR, 7.9;
P
<0.001), moderate anatomic complexity (AOR, 3.5;
P
=0.004), and patient weight <5 kg (AOR, 3.5;
P
=0.031).

Conclusions—

A diagnostic error taxonomy and knowledge of risk factors can assist in identification of targets for quality improvement initiatives that aim to decrease diagnostic error in pediatric echocardiography.
P-Selectin Glycoprotein Ligand-1 Is Highly Expressed on Ly-6C
hi
Monocytes and a Major Determinant for Ly-6C
hi
Monocyte Recruitment to Sites of Atherosclerosis in Mice
Authors: An Guangyu , Wang Huan , Tang Rong , Yago Tadayuki , McDaniel J. Michael , McGee Samuel , Huo Yuqing , Xia Lijun
Published: June 2008

Background—

Ly-6C
hi
monocytes are key contributors to atherosclerosis in mice. However, the manner in which Ly-6C
hi
monocytes selectively accumulate in atherosclerotic lesions is largely unknown. Monocyte homing to sites of atherosclerosis is primarily initiated by rolling on P- and E-selectin expressed on endothelium. We hypothesize that P-selectin glycoprotein ligand-1 (PSGL-1), the common ligand of P- and E-selectin on leukocytes, contributes to the preferential homing of Ly-6C
hi
monocytes to atherosclerotic lesions.

Methods and Results—

To test this hypothesis, we examined the expression and function of PSGL-1 on Ly-6C
hi
and Ly-6C
lo
monocytes from wild-type mice,
ApoE

−/−

mice, and mice lacking both
ApoE
and
PSGL-1
genes (
ApoE

−/−

/PSGL-1

−/−

). We found that Ly-6C
hi
monocytes expressed a higher level of PSGL-1 and had enhanced binding to fluid-phase P- and E-selectin compared with Ly-6C
lo
monocytes. Under in vitro flow conditions, more Ly-6C
hi
monocytes rolled on P-, E-, and L-selectin at slower velocities than Ly-6C
lo
cells. In an ex vivo perfused carotid artery model, Ly-6C
hi
monocytes interacted preferentially with atherosclerotic endothelium compared with Ly-6C
lo
monocytes in a PSGL-1–dependent manner. In vivo,
ApoE

−/−

mice lacking PSGL-1 had impaired Ly-6C
hi
monocyte recruitment to atherosclerotic lesions. Moreover,
ApoE

−/−

/PSGL-1

−/−

mice exhibited significantly reduced monocyte infiltration in wire injury–induced neointima and in atherosclerotic lesions.
ApoE

−/−

/PSGL-1

−/−

mice also developed smaller neointima and atherosclerotic plaques.

Conclusions—

These data indicate that PSGL-1 is a new marker for Ly-6C
hi
monocytes and a major determinant for Ly-6C
hi
cell recruitment to sites of atherosclerosis in mice.