bluuebunny/crossref_metadata_2025 huggingface dataset:
Causes and consequences of resource heterogeneity in forests: interspecific variation in light transmission by canopy trees
Authors: Canham Charles D. , Finzi Adrien C. , Pacala Stephen W. , Burbank Diane H.
Published: October 2007

We have analyzed the light transmission characteristics of the nine deciduous and coniferous species that dominate the transition oak–northern hardwood forests of southern New England. Maximum likelihood techniques were used to estimate species-specific light extinction coefficients, using fish-eye photography combined with data on the locations and geometry of trees in the neighborhood around each photo point. Quantum sensors were also used to quantify interspecific variation in the importance of sunflecks and beam enrichment. Variation in light extinction was closely correlated with shade tolerance and successional status of the species. The most shade-tolerant species (Fagusgrandifolia Ehrh. and Tsugacanadensis (L.) Carr.) cast the deepest shade (<2% of full sun), while earlier successional species such as Quercusrubra L. and Fraxinusamericana L. allowed greater light penetration (>5% full sun). These differences were more closely related to differences in crown depth than to differences in light extinction per unit depth of crown. Sunflecks contributed relatively little radiation beneath late successional species (<10% of total understory photosynthetically active radiation), but represented a major fraction (40–50%) of radiation beneath less shade-tolerant species. Using growth and mortality functions for the same species developed in a related study, our results indicate that saplings of all of the species have high survivorship in the shade cast by conspecific adults. However, only the three most shade-tolerant species have low rates of sapling mortality under the low light levels characteristic of stands dominated by late successional species. Our results are consistent with previously reported models, which propose that secondary succession is driven by interspecific differences in resource uptake and tolerance.
The impact of two harvesting systems on residual stems in a partially cut stand of northern hardwoods
Authors: Nichols M.T. , Lemin Jr. R.C . , Ostrofsky W.D.
Published: October 2007

Residual stand damage was evaluated following partial cutting with a mechanical and a conventional harvesting system in a northern hardwood stand in Maine. Damage from harvesting using a swing to bunch feller–buncher and grapple skidder was compared with damage from a chainsaw and cable skidder operation. Harvesting resulted in actual residual basal areas of 10 and 16.5 m2/ha in a heavy and light conventional treatment, respectively, and in 9 and 6.9 m2/ha in two mechanized treatments. The proportion of stems wounded averaged 22–44% in the conventional, and 20–31% in the mechanized operation. Wounds were significantly (p < 0.05) longer in the heavy conventional [Formula: see text] treatment than in light conventional [Formula: see text] and mechanized ([Formula: see text] and 60.2 cm) treatments. Wounds were located higher on the stems in the 9 m/ha mechanized [Formula: see text] than in the 10 m2/ha conventional treatment [Formula: see text]. A separate survey of the mechanized harvest showed that season of harvest (winter vs. summer) significantly affected wound location and the wound width to tree circumference ratio. A model was developed that relates harvesting treatment (light and heavy conventional and two heavy mechanical), species, distance of a stem from the edge a skid trail or access corridor, and initial stand basal area to the probability of injuring an individual stem. Mechanized harvesting using equipment with long-reach swing to bunch felling capability appears to be better than some other mechanical systems, and no worse than conventional harvesting systems, but the need to further reduce damage levels is evident.
Risk and the discount rate in forestry
Authors: Klemperer W. David , Cathcart James F. , Häring Thomas , Alig Ralph J.
Published: October 2007

One of the most common ways to account for investment risk is to add a risk premium to the risk-free discount rate when computing present values of expected revenues which are uncertain. Using certainty-equivalent analysis, we show that the correct risk premium for short-term investments can easily be in the commonly used 7-percentage-point range. But for such risk premiums to be appropriate for long-term forestry investments, the necessary certainty-equivalent conditions often seem to be unreasonably restrictive. Results suggest that the appropriate risk premium may decline with lengthening payoff period for many forest investments. Limited empirical data provide tentative support, but more research is needed to resolve the issue. We review policy implications and suggest areas for further research.
Effects of intermediate silvicultural treatments on the distribution of within-stand growth
Authors: Moore James A. , Zhang Lianjun , Newberry James D.
Published: October 2007

The distribution of within-stand basal area growth following silvicultural treatments was investigated using a relative size–relative growth (RSG) function. The effects of thinning on the distribution of tree basal area, including changes in location or scale, can be incorporated into the estimation of the RSG function parameters. Additional stand growth due to fertilization can also be allocated to individual trees using the same RSG function, since the contribution of a tree's response to total stand treatment response depends on its relative size in the stand. Statistical tests and validation of the RSG function indicated that thinning and fertilization do not alter the characteristic relationships between tree size, stand density, stand structure, and the relative distribution of growth across size classes within a stand. Therefore, silvicultural treatment growth responses predicted at a whole-stand level of resolution can be disaggregated to a list of individual trees using the RSG function developed from untreated plots.
Biogenesis pathway of pine chloroplast proteins encoded in the nucleus: import of pine proteins into spinach chloroplasts
Authors: Shinohara Kenji , Yamamoto Naoki , Mukai Yuzuru , Odani Keiji
Published: October 2007

Precursors to small subunits (SSU) of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco, EC 4.1.1.39) and apoproteins of light-harvesting chlorophyll a/b binding protein (LHCPII) in photosystem II were synthesized in vitro by expressing pine (Pinus thunbergii Parl.) cDNA clones encoding these proteins. The precursors to pine SSU and LHCPII were post-translationally transported into spinach chloroplasts, processed into mature size, and localized in only stroma and thylakoid membranes, respectively. The pine SSU was tightly integrated into spinach Rubisco; however, the pine LHCPII was not found in the light-harvesting chlorophyll–protein complex. These results suggest that a common biogenesis pathway of nuclear-encoded chloroplast proteins is present both in gymnosperms and in angiosperms.
Acid rain and soils of the Adirondacks. III. Rates of soil acidification in a montane spruce–fir forest at Whiteface Mountain, New York
Authors: Johnson A.H. , Friedland A.J. , Miller E.K. , Siccama T.G.
Published: October 2007

To assess the impact of atmospheric deposition on soil acidification and base cation supplies in montane spruce–fir forest soils at Whiteface Mountain, New York, base cation and proton fluxes were determined for organic and mineral horizons from measurements made at four stands (1020–1090 m above sea level) over a 4-year period. Our best estimates indicate an annual accumulation of H+ and a net loss of base cations from the forest floor of about 0.71 kmolc/ha, a 2.8% per year loss of the total forest floor base cation pool. This high rate of acidification is attributable to base cation leaching by sulfate and organic anions, and uptake by living biomass. From 1986 to 1990, the annual net loss rate of forest floor Ca, the most abundant base cation, was several times greater than historical loss rates as determined by 50-year comparisons of forest floor Ca in nearly identical forests of the Adirondack High Peaks region. Published data on long-term trends in Ca deposition in the U.S. Northeast suggest that the difference between historical and current net loss rates of forest floor Ca may be due to sharply reduced atmospheric inputs of Ca after about 1970, exacerbated by sulfate leaching. In mineral horizons where the total base cation pool (mostly mineral bound) is very large, the net losses of base cations were substantially lower and in the range where losses due to leaching and uptake can be countered by mineral weathering.
Genetic structure of western red cedar populations in the Interior West
Authors: Rehfeldt G.E.
Published: October 2007

Forty-one seedling populations of western red cedar (Thujaplicata Donn ex D. Don) were compared in five environmentally disparate common gardens. Separate tests of 25 wind-pollinated families from a single population were conducted on two of the sites. Genetic differences among populations and families were detected for variables related to growth and winter hardiness. Statistically significant multiple regression models with R2 values as high as 0.53 related genetic variation among populations to the elevation and geographic origin of the seed. The slope of the clines, however, was so gentle that populations must be separated by about 600 m in elevation or by 2° latitude before one can be reasonably certain of genetic differentiation. While genetic variation among families suggests that gains in the growth of western red cedar can be made through tree breeding, establishing evaluation trials for estimating genetic variances, breeding values, and responses to selection is problematic on sites in the interior.
Water-stress tolerance of black and eastern cottonwood clones and four hybrid progeny. II. Metabolites and inorganic ions that constitute osmotic adjustment
Authors: Tschaplinski T.J. , Tuskan G.A.
Published: October 2007

The biochemical bases of water-stress tolerance in a pedigree consisting of black cottonwood (Populustrichocarpa Torr. & Gray female) and eastern cottonwood (Populusdeltoides Bartr. male) parental clones and four hybrid progeny were investigated. Trees were grown outdoors in pots; well-watered trees (soil water potential greater than −0.03 MPa) were kept moist in trays, and stressed trees (soil water potential less than −2.0 MPa) were subjected to repeated cyclical stress of 1 or 2 days duration over the 14-week study. Analysis of the major metabolites and ions in fully expanded leaves demonstrated that the greatest degree of osmotic adjustment was displayed by male hybrid 242, the P. deltoides male parent, and male hybrid 239 to a lesser extent. Osmotic adjustment in leaves of both hybrid 242 and the P. deltoides male parent was primarily constituted by malic acid, K, sucrose, and glucose, with the same metabolites also increasing in fine roots of hybrid 242, the only clone to display osmotic adjustment in roots. Female clone 240 and P. deltoides displayed organic solute-based adjustments to water stress that were offset by declines in inorganic ions, particularly Na and Mg. Given that the P. trichocarpa female parent did not display osmotic adjustment in either tissue, the hybrids' capacity for adjustment was likely conferred by the P. deltoides male parent.
Bark properties and fire resistance of selected tree species from the central hardwood region of North America
Authors: Hengst Gretel E. , Dawson Jeffrey O.
Published: October 2007

Some physical, thermal, and chemical properties of bark of 16 tree species native to the central hardwood region were measured to determine their potential to protect the vascular cambium from damage by fire. The relationship between DBH and bark thickness for each of 16 species was determined. For purposes of monitoring seasonal trends, two species (Quercusmacrocarpa Michx. and Acersaccharinum L.) were sampled periodically during one growing season. Temperature response to bark surface heating of 11 species was monitored at the cambial layer during simulated fires conducted in the field. Bark samples were analyzed for moisture content, specific gravity, dry weight, volatile matter content, and time until ignition. Overall, during simulated fires, temperature gradients were decreased and maximum cambial temperatures were reduced as bark thickness increased. Thick-barked species had lower maximum cambial temperatures, longer times to reach peak temperatures, slower rates of heat loss, and shorter time until surface ignition. Populusdeltoides Marsh, was the most heat resistant among species tested, while Acersaccharinum was the least. Higher specific gravities were associated with higher rates at which cambial temperatures rose as well as with increased time required for surface ignition.
Genetic variation of Pinuscontorta var. latifolia breeding material in Sweden
Authors: Ericsson Tore , Danell Öje , Andersson Bengt
Published: October 2007

Genetic parameters were estimated, using the restricted maximum likelihood method, for 1112 open-pollinated progenies of Pinuscontorta Dougl. ex Loud. var. latifolia Engelm. plus trees selected from among 83 undisturbed stands in the interior of the Yukon and British Columbia, and five similar stands in Alberta. The progenies were grown in Swedish test plantations. Tree condition, height, and ramicorn whorl frequency were assessed at ages ranging between 8 and 12 years. On the harshest sites, weather and fungal damage, e.g., caused by Gremmeniellaabietina (Lagerb.) Morelet, were also assessed. Categorical data were transformed into values on a normal score scale to improve the efficiency of the evaluation. The genetic coefficients of variation in tree height ranged between 8 and 17%. The heritabilities for tree height, including stand genetic variation, were estimated to range between 0.10 and 0.54. Genetic correlations between tree height and trunk leaning were usually high and positive, as were correlations between height and ramicorn whorl frequency. At one site, heritability estimates for trunk injury and (or) canker and fungal and (or) weather damage were 0.12 and 0.18, respectively.
Crown development in red pine stands. I. Absolute and relative growth measures
Authors: Larocque Guy R. , Marshall Peter L.
Published: October 2007

The crown development of red pine (Pinusresinosa Ait.) plantations originating from different initial spacings was studied between 13 and 33 years of age. First, the effect of spacing on models used to predict crown width and crown ratio from diameter at breast height (DBH) and height was examined. Models for trees of different ages that included all the spacings were found to predict crown growth measures as well as separate models derived for each spacing. Second, the following crown relative growth measures were studied: crown width/crown length (crown shape ratio), crown surface/crown volume, and foliage biomass/crown volume. The way such measures changed over time under different initial spacings was studied; these findings were compared with changes in relative growth rate (RGR), which can be used to evaluate the effect of competitive stress. Crown shape ratio decreased with an increase in DBH in the absence of severe competition, and increased with DBH under severe competitive stress. The other two crown relative growth measures were always negatively correlated with DBH; this shows that large trees use their aerial growing space less efficiently than small trees at all stages of stand development. Only crown shape ratio changed in the same way as RGR.
Crown development in red pine stands. II. Relationships with stem growth
Authors: Larocque Guy R. , Marshall Peter L.
Published: October 2007

The development of red pine (Pinusresinosa Ait.) stands originating under different initial spacings was examined using three measures of growth efficiency that are similar in concept to relative growth rate: diameter at breast height (DBH) increment/crown width, DBH increment/crown projection, and DBH increment/foliage biomass. These three measures of efficiency decreased with increasing DBH in the absence of severe competition and increased with increasing DBH under severe competitive stress. This indicates that small trees occupied their aerial growing space better and utilized their foliage to produce stemwood more efficiently than large trees in the absence of competition, and that the effect of competition was to reverse this trend. Absolute and relative growth rates for DBH and the three measures of growth efficiency were related very significantly to absolute (e.g., crown width) and relative (e.g., crown width/crown length) measures of crown development.
Foliar nutrient status and fascicle weight of lodgepole pine after nitrogen and sulphur fertilization in the interior of British Columbia
Authors: Brockley R.P. , Sheran F.J.
Published: October 2007

The effects of nitrogen and nitrogen + sulphur fertilization on the first-year fascicle weight and foliar nutrient status of immature, thinned lodgepole pine (Pinuscontorta Dougl. var. latifolia Engelm.) were evaluated at seven locations in the interior of British Columbia. The results indicate that sulphur deficiencies, either aggravated or induced by nitrogen fertilization, may limit the responsiveness of lodgepole pine to nitrogen additions. At four locations, combined sulphur and nitrogen additions improved the sulphur status of fertilized trees and significantly increased the weight of fascicles produced during the first year after treatment compared with that achieved with nitrogen alone. Ammonium sulphate was a superior sulphur source compared with elemental sulphur–sodium bentonite prills and also was readily taken up by trees. The oxidation of the elemental sulphur prills was apparently too slow to satisfy sulphur requirements in the first year. Increasing the sulphur application rate from 50 to 100 kg/ha generally gave only small improvements in first-year fascicle weight response despite a significant improvement in foliar sulphur concentration and content. The responsiveness to sulphur fertilization was not consistent across all sites. Further characterization of sites that are responsive and unresponsive to sulphur additions is needed to more accurately diagnose sulphur deficiencies and predict responsiveness to sulphur additions.
Evaluation of root oxygenation and growth in baldcypress in response to short-term soil hypoxia
Authors: Kludze Hillarius K. , Pezeshki S. Reza , Delaune Ronald D.
Published: October 2007

Seedlings of baldcypress (Taxodiumdistichum (L.) Rich. var. distichum) were grown under laboratory and greenhouse conditions to determine the extent to which short-term soil hypoxia influences root aerenchyma–air space formation (expressed as a percentage of total root volume) and concomitant radial oxygen loss. Subsequent photosynthesis and growth responses were also determined. A colorimetric technique involving the use of Ti3+-citrate, a strong reducing compound, was used to quantify radial oxygen loss from whole root system. Soil redox potential of −250 ± 10 mV resulted in enhancement of both root porosity and radial oxygen loss as much as 3-fold compared with plants under well aerated conditions (515 ± 25 mV). The mean oxygen loss from roots was 1.4 mmol O2•g−1•day−1 in drained plants and 4.6 mmol O2•g−1•d−1 in flooded plants. Mean root porosity was 13.3 and 41.4% in drained and flooded plants, respectively. Stomatal conductance, net photosynthesis, and height growth were adversely affected by reduced soil conditions. Baldcypress exhibited an avoidance mechanism under reduced soil conditions by increasing aerenchyma formation and rhizosphere oxygenation at young ages. This may explain the significance of flooding episodes encountered in young stages in enabling baldcypress saplings and trees to tolerate flooding in later stages of the life cycle.
Effects of the frequency, timing, and intensity of simulated browsing on growth and mortality of tree seedlings
Authors: Canham Charles D. , McAninch Jay B , Wood David M.
Published: October 2007

Field exclosure studies have shown that mammalian browsers such as white-tailed deer (Odocoileusvirginianus) can have pervasive effects on forest dynamics in eastern North America. Direct experimental tests of the effects of browsing on growth and survival of a wide range of tree species, however, have yielded conflicting results. This study was designed to assess the effects of variation in the frequency, seasonal timing, and intensity of browsing (simulated by mechanical clipping) on the growth and mortality of three of the major tree species of the Hudson Valley, New York. The clipping treatments were applied to seedlings grown under two different light regimes (full sun and 8% of full sun) to examine seedling responses under different levels of shade-induced carbon stress. Our results demonstrate that even 2 successive years of heavy winter clipping (75% of new shoot growth removed) has little immediate effect on growth or survival of any of the three species. It is possible that winter browsing only has significant negative effects when seedlings are browsed repeatedly over long periods of time. However, comparable levels of summer browsing for only 2 years significantly reduced both growth and survival of all three species. While most natural browsing occurs in the dormant season, our results suggest that it is the less frequent browsing during late spring and early summer that has the greatest immediate effect on tree seedlings. Shading reduced growth and increased mortality in all three species; however, there was only a limited interaction between light level and the simulated browsing treatments. The effects of browsing on survival were similar in all three species; however, the effects of browsing on cumulative height and annual growth varied enough among the species to suggest that browsing could cause significant variation among these species in their rate of invasion in old fields and rights of way, and their rate of regeneration following logging or disturbance of forests.
Seedling responses to forest canopy disturbance following a spruce budworm outbreak in Maine
Authors: Osawa Akira
Published: October 2007

Patterns of tree mortality and seedling responses to canopy disturbance were investigated in northern Maine, where an outbreak of the spruce budworm (Choristoneurafumiferana (Clem.)) affected the forests of balsam fir (Abiesbalsamea (L.) Mill.) and spruce (Picea spp.) continuously between 1972 and 1984. The outbreak created a gradient of canopy tree mortality that ranged between 8.5 and 100% of the cumulative basal area in 1984. This was a result of the difference in vulnerability among the host species (balsam fir > spruce) and of their spatial distribution patterns along the site drainage gradient. Two groups of plant species responded differently to the gradient of canopy disturbance: balsam fir, spruce, and white birch (Betulapapyrifera Marsh.) regenerated mostly at the intermediate levels of mortality (≈20%by basal area) of the canopy balsam fir; raspberry (Rubusidaeus L.) and pin cherry (Prunuspensylvanica L.) were most abundant at ≈100% fir mortality. Overall, the observed responses in space and time of the seedlings to budworm-caused canopy disturbance could be mostly explained by the concept of patch dynamics. Long-term changes in species composition of the spruce–fir forests cannot be predicted with precision with the present knowledge. However, I hypothesize, based on the species-specific vulnerability to budworm damage and patterns of regeneration, that the proportion of spruce to fir trees would not differ very much in the long run regardless of extensive tree mortality by the spruce budworm.
Current approaches for assessing insulin sensitivity and resistance in vivo: advantages, limitations, and appropriate usage
Authors: Muniyappa Ranganath , Lee Sihoon , Chen Hui , Quon Michael J.
Published: October 2007

Insulin resistance contributes to the pathophysiology of diabetes and is a hallmark of obesity, metabolic syndrome, and many cardiovascular diseases. Therefore, quantifying insulin sensitivity/resistance in humans and animal models is of great importance for epidemiological studies, clinical and basic science investigations, and eventual use in clinical practice. Direct and indirect methods of varying complexity are currently employed for these purposes. Some methods rely on steady-state analysis of glucose and insulin, whereas others rely on dynamic testing. Each of these methods has distinct advantages and limitations. Thus, optimal choice and employment of a specific method depends on the nature of the studies being performed. Established direct methods for measuring insulin sensitivity in vivo are relatively complex. The hyperinsulinemic euglycemic glucose clamp and the insulin suppression test directly assess insulin-mediated glucose utilization under steady-state conditions that are both labor and time intensive. A slightly less complex indirect method relies on minimal model analysis of a frequently sampled intravenous glucose tolerance test. Finally, simple surrogate indexes for insulin sensitivity/resistance are available (e.g., QUICKI, HOMA, 1/insulin, Matusda index) that are derived from blood insulin and glucose concentrations under fasting conditions (steady state) or after an oral glucose load (dynamic). In particular, the quantitative insulin sensitivity check index (QUICKI) has been validated extensively against the reference standard glucose clamp method. QUICKI is a simple, robust, accurate, reproducible method that appropriately predicts changes in insulin sensitivity after therapeutic interventions as well as the onset of diabetes. In this Frontiers article, we highlight merits, limitations, and appropriate use of current in vivo measures of insulin sensitivity/resistance.
vocd: A theoretical and empirical evaluation
Authors: McCarthy Philip M. , Jarvis Scott
Published: October 2007

A reliable index of lexical diversity (LD) has remained stubbornly elusive for over 60 years. Meanwhile, researchers in fields as varied as stylistics, neuropathology, language acquisition, and even forensics continue to use flawed LD indices — often ignorant that their results are questionable and in some cases potentially dangerous. Recently, an LD measurement instrument known as vocd has become the virtual tool of the LD trade. In this paper, we report both theoretical and empirical evidence that calls into question the rationale for vocd and also indicates that its reliability is not optimal. Although our evidence shows that vocd's output (D) is a relatively robust indicator of the aggregate probabilities of word occurrences in a text, we show that these probabilities — and thus also D — are affected by text length. Malvern, Richards, Chipere and Durán (2004) acknowledge that D (as calculated by vocd's default method) can be affected by text length, but claim that the effects are not significant for the ranges of text lengths with which they are concerned. In this paper, we explain why D is affected by text length, and demonstrate with an extensive empirical analysis that the effects of text length are significant over certain ranges, which we identify.
Students' voices in the evaluation of their written summaries: Empowerment and democracy for test takers?
Authors: Guoxing Yu
Published: October 2007

Two kinds of scoring templates were empirically derived from summaries written by experts and students to evaluate the quality of summaries written by the students. This paper reports students' attitudes towards the use of the two templates and its differential statistical effects on the judgment of students' summarization performance. It was found that a summary consistently received higher scores when judged by the popular template, regardless of the language and the language order (English then Chinese or Chinese then English) in which a summary was produced. However, the scores from the expert template were slightly better predictors of students' reading abilities as measured by FCE and TOEFL. The majority of the students strongly preferred the expert template. Their arguments centered mainly on the differences between students and experts in their language abilities and experience, their stereotypical status in educational assessment, and the dialectical interpretations of `quantity' and `quality'. Implications of these findings are discussed with specific reference to the value of involving test-takers in assessment criteria development.
Peptostreptococcus micros cell wall elicits a pro-inflammatory response in human macrophages
Authors: Tanabe Shin-ichi , Bodet Charles , Grenier Daniel
Published: October 2007

Peptostreptococcus micros is a Gram-positive anaerobic bacterium associated with periodontitis, a chronic inflammatory disease affecting tooth-supporting tissues. In the present study, we investigated the response of human macrophages to stimulation with a cell wall preparation from P. micros. In addition, the effect of the preparation on the phosphorylation of macrophage kinases was studied. The preparation, which was non-toxic for macrophages, significantly increased the secretion of the pro-inflammatory cytokines TNF-α, IL-1β and IL-6. It also increased the secretion of two potent chemokines IL-8 and, to a lesser extent, RANTES. Lastly, stimulation of macrophages by the P. micros cell wall preparation induced a significant increase in MMP-9 secretion but had no effect on the production of prostaglandin E2. The phosphorylation of macrophage kinases, including cAMP-dependent protein-serine kinase (PKA) catalytic subunit beta, G protein-coupled receptor-serine kinase 2, mitogen-activated protein-serine kinase p38 alpha (p38a MAPK), extracellular regulated protein-serine kinase 2 (ERK2) and Jun N-terminus protein-serine kinases (JNK), increased following stimulation with cell wall. In summary, our study showed that the P. micros cell wall preparation induced intracellular signaling pathways, leading to an increased production of pro-inflammatory cytokines, chemokines and MMP-9 by macrophages.
High glucose up-regulates lipopolysaccharide-stimulated inflammatory cytokine production via c-jun N-terminal kinase in the monocytic cell line THP-1
Authors: Iwata Hirotaka , Soga Yoshihiko , Meguro Michio , Yoshizawa Sayuri , Okada Yuka , Iwamoto Yoshihiro , Yamashita Akiko , Takashiba Shogo , Nishimura Fusanori
Published: October 2007

Diabetic subjects are susceptible to atherosclerosis. It has been postulated that inflammation plays a crucial role in atherogenesis. Since previous studies suggested persistent low-grade infection by Gram-negative bacteria such as Chlamydia spp. and/or periodontal infection is associated with increased atherogenesis among diabetic subjects, we hypothesized that macrophages under hyperglycemia respond to lipopolysaccharide (LPS) challenge in a more exaggerated manner than under normal glucose conditions. Therefore, we examined cytokine productivity and associated signal transduction molecules in LPS-stimulated the monocytic cell line THP-1, under conditions of hyperglycemia. Differentiated THP-1 cells were cultured under normal and high glucose conditions without fetal bovine serum, and were stimulated with Escherichia coli LPS in the presence of LPS binding protein. Following stimulation, activated signal transduction molecules were detected by protein microarray and confirmed thereafter. Results indicated that c-jun N-terminal kinase (JNK) was highly-phosphorylated at high glucose concentrations, and this was confirmed by Western-immunoblotting. Tumor necrosis factor-α and monocyte chemo-attractant protein-1 production were significantly enhanced under these conditions. SP600125, a selective inhibitor of JNK, dose-dependently suppressed the production of these cytokine. Therefore, we suggest that this may be one of the mechanisms by which sub-clinical infection by Gram-negative bacteria promotes atherosclerosis in diabetic subjects.
IEIIS Meeting minireview: Bordetella evolution: lipid A and Toll-like receptor 4
Authors: MacArthur Iain , Mann Paul B. , Harvill Eric T. , Preston Andrew
Published: October 2007

The evolution of Bordetella pertussis and Bordetella parapertussis from Bordetella bronchiseptica involved changes in host range and pathogenicity. Recent data suggest that the human-adapted Bordetella modified their interaction with host immune systems to effect these changes and that decreased stimulation of Toll-like receptor 4 (TLR4) by lipid A is central to this. We discuss Bordetella lipid A structure and genetics within the context of evolution and host immunity.
Nothing to Hide, Nothing to Fear?
Authors: Saetnan Ann Rudinow
Published: October 2007

Demand for surveillance technologies often assumes that these technologies would accurately identify those guilty of crimes and only those guilty of crimes. But how accurate are surveillance technologies as “diagnostic” tools? Surveillance technologies have not been tested for accuracy in the manner we expect for medical diagnostic technologies. Tests of medical technologies are designed to address sensitivity (How many of those affected by a disease does the test identify?) and specificity (How many unaffected by the disease does the test show as healthy?). Even for tests with more than 90% sensitivity and specificity, the majority of test positive results are false. Using value estimates for facial recognition and DNA identification, this article estimates the answers to these questions for crime surveillance technologies. The vast majority of test positive results would be false. In other words, even those of us with “nothing to hide” may have much to fear from crime surveillance technologies.
Prevention of Child Sexual Abuse: Evaluation of a Community Media Campaign
Authors: Rheingold Alyssa A. , Campbell Carole , Self-Brown Shannon , de Arellano Michael , Resnick Heidi , Kilpatrick Dean
Published: October 2007

Given that mass media techniques have been an effective tool within the public health field for affecting behavioral change, these strategies may prove successful for the primary prevention of child sexual abuse (CSA). This study was an independent evaluation of a CSA media campaign. Two hundred parents were recruited from eight sites across the United States. Results indicated that the combined mass media campaign affected knowledge about CSA at the time of intervention compared to no intervention. No significant differences were found in regards to CSA attitudes. A significant positive impact on primary prevention response behaviors assessed using hypothetical vignettes was found; however, no significant findings were noted for several other behavioral responses. Knowledge and behavioral gains were not maintained at the one-month follow-up. Small sample size at follow-up may have affected findings. Results of this study imply that media campaigns alone may not significantly affect primary prevention of CSA.
Psychosocial Characteristics of Nonoffending Mothers of Sexually Abused Girls: Findings From a Prospective, Multigenerational Study
Authors: Kim Kihyun , Noll Jennie G. , Putnam Frank W. , Trickett Penelope K.
Published: October 2007

This study examined psychosocial characteristics of nonoffending mothers of sexually abused girls. The sample consisted of 72 ethnically diverse mothers of sexually abused girls aged 6 to 16 years, and 55 mothers of girls who were demographically similar with the abused girls on age, socioeconomic status, and family constellation. The variables examined included measures of the mothers' childhood developmental histories and current functioning (e.g., depression, parenting), as well as their current family environment. The specific questions addressed were (a) whether mothers of sexually abused girls could be distinguished from mothers of comparison girls on various psychosocial characteristics and (b) whether three subgroups of mothers (i.e., mother and daughter sexually abused, daughter-only abused, neither mother nor daughter abused) would exhibit different patterns of psychosocial characteristics. Results show that nonoffending mothers of sexually abused girls may confront considerable psychosocial challenges following the disclosure of their daughters' sexual abuse and that mother's own childhood abuse experiences may be an important factor to understand these challenges.
Commentary on Bishop
Authors: Ernst Edzard
Published: October 2007

Complementary and alternative medicine (CAM) is more popular than ever before; at least this is what syrvey data seems to imply, yet we need to keep in mind that, for a range of reasons, such data are notoriously soft. CAM is by no means a well-defined entity; the prevalence of and reasons for using acupuncture are almost certainly different from those relating to crystal healing. Moreover, we tend to forget that virtually none of the questionnaires used to study these phenomeana are validated, and we all know that answers depend on how questions are being formulated. It seems to follow that surveys are of only limited value and might even distract us from the much more important question whether CAM generates more good than harm.
Relationships between Felt Age and Perceived Disability, Satisfaction with Recovery, Self-efficacy Beliefs and Coping Strategies
Authors: Boehmer Sonja
Published: October 2007

Subjective age is related to health and to life satisfaction, and adaptation to stressful life events is associated with self-efficacy beliefs and coping. The present study on cancer survivors addressed two objectives: the relationship between felt age and perceived disability and satisfaction with recovery, and the feeding back of felt age on general self-efficacy beliefs and coping strategies. Data were collected one and six months after surgery. Individuals with younger age identities reported lower levels of perceived disability and avoidance-oriented coping and higher levels of satisfaction with recovery, self-efficacy and meaning-focused coping than individuals with older age identities. Individuals with decreased or stable felt age indicated increased meaning-focused coping or avoidance-oriented coping, respectively. Explanations for these associations are discussed.
Experimental and Analytical Investigation of Moisture Movement in Clothing
Authors: Takada S. , Hokoi S. , Kumaran M.K.
Published: October 2007

In order to design an efficient air-conditioning system, the specifics of the transient thermal and physiological responses of a human body to the hygrothermal environment should be taken into account. This response will strongly depend on the behavior of heat and moisture transport, and moisture accumulation in the clothing, especially when sweat exists in and around the clothing. As a basic information on this problem, a model of the moisture transfer in cloth is necessary. In this article, a model of the liquid moisture movement in clothing under gravity is developed and applied, based on a diffusion model. Firstly, the moisture diffusivity is determined from the investigation of the moisture absorption process in the horizontal direction where gravity has no influence on the moisture movement. Secondly with the use of the moisture diffusivity thus determined, a moisture absorption process in the upward direction against gravity is investigated. The validity of the parameter related to the gravity effect is examined by comparing the results of numerical calculations with the experimental results obtained from the gamma-ray method. Since the two agree generally well, the parameters namely liquid moisture diffusivity and sorption isotherm derived here for a sample of broadcloth are considered reliable.
Brick Cavity Walls: A Performance Analysis Based on Measurements and Simulations
Authors: Hens H. , Janssens A. , Depraetere W. , Carmeliet J. , Lecompte J.
Published: October 2007

After world war two, cavity walls became a widespread external wall type in the cool but humid climate of North Western Europe. Moisture tolerance of the unfilled construction was excellent. Instead, calculation and testing underlined that the unfilled cavity walls of that era performed poorly from a thermal insulation point of view. After the energy crisis of 1973, cavity filling was therefore introduced as the main upgrade. Hence, extensive testing revealed upgrading was less simple than expected. Air in- and exfiltration through the wall, wind washing behind the fill, thermal stack induced air looping around the fill and thermal bridging all cooperated in lowering expected thermal quality of the filled walls. Anyhow, at the same time testing underlined that moisture tolerance remained outstanding in the cool, humid climate of North Western Europe also without cavity ventilation. That resulted in a set of recommendations how to construct high performing filled cavity walls.
Bioinformatic identification of novel putative photoreceptor specific cis-elements
Authors: Danko Charles G , McIlvain Vera A , Qin Maochun , Knox Barry E , Pertsov Arkady M
Published: October 2007

Background

Cell specific gene expression is largely regulated by different combinations of transcription factors that bind cis-elements in the upstream promoter sequence. However, experimental detection of cis-elements is difficult, expensive, and time-consuming. This provides a motivation for developing bioinformatic methods to identify cis-elements that could prioritize future experimental studies. Here, we use motif discovery algorithms to predict transcription factor binding sites involved in regulating the differences between murine rod and cone photoreceptor populations.

Results

To identify highly conserved motifs enriched in promoters that drive expression in either rod or cone photoreceptors, we assembled a set of murine rod-specific, cone-specific, and non-photoreceptor background promoter sequences. These sets were used as input to a newly devised motif discovery algorithm called Iterative Alignment/Modular Motif Selection (IAMMS). Using IAMMS, we predicted 34 motifs that may contribute to rod-specific (19 motifs) or cone-specific (15 motifs) expression patterns. Of these, 16 rod- and 12 cone-specific motifs were found in clusters near the transcription start site. New findings include the observation that cone promoters tend to contain TATA boxes, while rod promoters tend to be TATA-less (exempting Rho and Cnga1). Additionally, we identify putative sites for IL-6 effectors (in rods) and RXR family members (in cones) that can explain experimental data showing changes to cell-fate by activating these signaling pathways during rod/cone development. Two of the predicted motifs (NRE and ROP2) have been confirmed experimentally to be involved in cell-specific expression patterns. We provide a full database of predictions as additional data that may contain further valuable information. IAMMS predictions are compared with existing motif discovery algorithms, DME and BioProspector. We find that over 60% of IAMMS predictions are confirmed by at least one other motif discovery algorithm.

Conclusion

We predict novel, putative cis- elements enriched in the promoter of rod-specific or cone-specific genes. These are candidate binding sites for transcription factors involved in maintaining functional differences between rod and cone photoreceptor populations.
Growing functional modules from a seed protein via integration of protein interaction and gene expression data
Authors: Maraziotis Ioannis A , Dimitrakopoulou Konstantina , Bezerianos Anastasios
Published: October 2007

Background

Nowadays modern biology aims at unravelling the strands of complex biological structures such as the protein-protein interaction (PPI) networks. A key concept in the organization of PPI networks is the existence of dense subnetworks (functional modules) in them. In recent approaches clustering algorithms were applied at these networks and the resulting subnetworks were evaluated by estimating the coverage of well-established protein complexes they contained. However, most of these algorithms elaborate on an unweighted graph structure which in turn fails to elevate those interactions that would contribute to the construction of biologically more valid and coherent functional modules.

Results

In the current study, we present a method that corroborates the integration of protein interaction and microarray data via the discovery of biologically valid functional modules. Initially the gene expression information is overlaid as weights onto the PPI network and the enriched PPI graph allows us to exploit its topological aspects, while simultaneously highlights enhanced functional association in specific pairs of proteins. Then we present an algorithm that unveils the functional modules of the weighted graph by expanding a kernel protein set, which originates from a given 'seed' protein used as starting-point.

Conclusion

The integrated data and the concept of our approach provide reliable functional modules. We give proofs based on yeast data that our method manages to give accurate results in terms both of structural coherency, as well as functional consistency.
Molecular characterization, gene expression and dependence on thyroid hormones of two type I keratin genes (sseKer1 and sseKer2) in the flatfish Senegalese sole (Solea senegalensisKaup)
Authors: Infante Carlos , Manchado Manuel , Asensio Esther , Cañavate José Pedro
Published: October 2007

Background

Keratins make up the largest subgroup of intermediate filaments, and, in chordates, represent the most abundant proteins in epithelial cells. They have been associated with a wide range of functions in the cell, but little information is still available about their expression profile and regulation during flatfish metamorphosis. Senegalese sole (Solea senegalensis) is a commercially important flatfish in which no keratin gene has been described yet.

Results

The development of large-scale genomics of Senegalese sole has facilitated the identification of two different type I keratin genes referred to as sseKer1 and sseKer2. Main characteristics and sequence identities with other fish and mammal keratins are described. Phylogenetic analyses grouped sseKer1 and sseKer2 in a significant clade with other teleost epidermal type I keratins, and have allowed for the identification of sseKer2 as a novel keratin. The expression profile of both genes was studied during larval development and in tissues using a real-time approach. sseKer1 and sseKer2 mRNA levels were significantly higher in skin than in other tissues examined. During metamorphosis, sseKer1 transcripts increased significantly at first stages, and reduced thereafter. In contrast, sseKer2 mRNA levels did not change during early metamorphosis although a significant drop at metamorphosis climax and late metamorphosis was also detected. To study the possible regulation of sseKer gene expressions by thyroid hormones (THs), larvae were exposed to the goitrogen thiourea (TU). TU-treated larvae exhibited higher sseKer1 and sseKer2 mRNA levels than untreated control at both 11 and 15 days after treatment. Moreover, addition of exogenous T4 hormone to TU-treated larvae restored or even reduced the steady-state levels with respect to the untreated control, demonstrating that expression of both genes is negatively regulated by THs.

Conclusion

We have identified two keratin genes, referred to as sseKer1 and sseKer2, in Senegalese sole. Phylogenetic analyses revealed sseKer2 as a novel keratin. Although they exhibit different expression patterns during larval development, both of them are negatively regulated by THs. The co-regulation by THs could explain the reduction of both keratin transcripts after the metamorphosis climax, suggesting their role in the tissue remodelling processes that occur during metamorphosis.