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PubMed2005

Occurrence of nodulation in unexplored leguminous trees native to the West African tropical rainforest and inoculation response of native species useful in reforestation.

Despite the abundance and diversity of timber tree legumes in the West African rainforest, their ability to form nitrogen-fixing nodules in symbiosis with rhizobia, and their response to rhizobial inoculation, remain poorly documented. In the first part of this study the occurrence of nodulation was determined in 156 leguminous species growing in six natural forest areas in Guinea, mostly mature trees. In the second part, an in situ experiment of rhizobial inoculation was performed on eight selected tree species belonging to three genera: Albizia, Erythrophleum and Millettia. Of the 97 plant species and 14 genera that had never been examined before this study, 31 species and four genera were reported to be nodulated. After 4 months of growing in a nursery and a further 11 months after transplantation of plants to the field, we observed a highly significant (P < 0.001) and positive effect of inoculation with Bradyrhizobium sp. strains on the growth of the eight tree species tested. The importance of determining the nodulation ability of unexplored local trees and subsequently using this information for inoculation in reforestation programmes was demonstrated.

Bradyrhizobium↗
PubMed2006

Wood mechanics, allometry, and life-history variation in a tropical rain forest tree community.

Wood density plays a central role in the life-history variation of trees, and has important consequences for mechanical properties of wood, stem and branches, and tree architecture. Wood density, modulus of rupture, modulus of elasticity, and safety factors for buckling and bending were determined for saplings of 30 Bolivian rain forest tree species, and related to two important life-history axes: juvenile light demand and maximum adult stature. Wood density was strongly positively related to wood strength and stiffness. Species safety factor for buckling was positively related to wood density and stiffness, but tree architecture (height : diameter ratio) was the strongest determinant of mechanical safety. Shade-tolerant species had dense and tough wood to enhance survival in the understorey, whereas pioneer species had low-density wood and low safety margins to enhance growth in gaps. Pioneer and shade-tolerant species showed opposite relationships between species traits and adult stature. Light demand and adult stature affect wood properties, tree architecture and plant performance in different ways, contributing to the coexistence of rain forest species.

Biometry↗
PubMed2006

Effects of the surrounding matrix on tree recruitment in Amazonian forest fragments.

Little is known about how the surrounding modified matrix affects tree recruitment in fragmented forests. We contrasted effects of two different matrix types, Vismia- and Cecropia-dominated regrowth, on recruitment of pioneer tree species in forest fragments in central Amazonia. Our analyses were based on 22, 1-ha plots in seven experimental forest fragments ranging in size from 1 to 100 ha. By 13 to 17 years after fragmentation, the population density of pioneer trees was significantly higher in plots surrounded by Vismia regrowth than in plots surrounded by Cecropia regrowth, and the species composition and dominance of pioneers differed markedly between the two matrix types. Cecropia sciadophylla was the most abundant pioneer in fragments surrounded by Cecropia regrowth (constituting nearly 50% of all pioneer trees), whereas densities of species in Vismia-surrounded fragments were distributed more evenly. Thus the surrounding matrix had a strong influence on patterns of tree recruitment in Amazonian forest fragments.

Conservation of Natural Resources↗
PubMed2006

Fire and green-tree retention in conservation of red-listed and rare deadwood-dependent beetles in Finnish boreal forests.

Habitat loss, fragmentation, and declining habitat quality have created an extinction debt in boreal forests, which could be partly reversed by deliberately improving the habitat quality in managed areas outside reserves. We studied the effects of green-tree retention and controlled burning on red-listed and rare, deadwood-dependent (saproxylic) beetles in a large-scale field experiment in eastern Finland. Our factorial study design included 24 sites dominated by Scots pine (Pinus sylvestris L.) and with three levels of green-tree retention (0, 10, and 50 m3/ha) and uncut controls. Twelve of the 24 sites were burned in 2001. We sampled beetles with 10 flight-intercept traps on each site during the years 2000-2002 (i.e., 1 pretreatment and 2 post-treatment years). A total sample of 153,449 individuals representing 1,160 beetle species yielded 2,107 specimens of 84 red-listed or rare saproxylic species. The richness of these species was higher on the burned than on the unburned sites, and higher levels of green-tree retention promoted species richness, but there were clear differences between the years. The richness of red-listed and rare saproxylic species increased in the first post-treatment year, evidently due to the treatments, continued to increase on the burned sites in the second post-treatment year, but decreased on the unburned sites. Our results showed that the living conditions of many red-listed and rare saproxylic species could be improved significantly with rather simple alterations to forest management methods. Controlled burning with high levels of green-tree retention creates resources for many saproxylic species, but increasing the levels of green-tree retention in unburned areas can also be beneficial.

Animals↗
PubMed2006

Suicide attempts among substance use disorder patients: an initial step toward a decision tree for suicide management.

BACKGROUND: Little empirical data are available to develop profiles of patients who attempt suicide or to formulate a decision tree for suicide management. This study identifies profiles of patients who have a high risk of suicide attempt and takes a first step toward developing a decision tree to classify high-risk patients. METHODS: Based on a cross-sectional, nationwide cohort of substance use disorder patients (N=34,251) in 150 Veterans Affairs (VA) facilities, a total of 5,671 patients who reported suicidal ideation in the 30 days before intake assessment were included in receiver operating characteristic (ROC) analyses to identify the 30-day risk of an actual suicide attempt. Clinical diagnostic and Addiction Severity Index interview data were used. RESULTS: Results provide an initial decision tree to classify high-risk patients with sensitivity ranging from 0.33 to 0.89, and specificity, from 0.42 to 0.87. The factors included in the decision tree encompass history of prior suicide attempts, current drinking to intoxication, current cocaine use, first occasion of suicidal ideation, and difficulty controlling violent behavior. CONCLUSIONS: To our knowledge, this is the first attempt to use empirical data to provide information to eventually establish a decision tree for clinical management of patients with suicidal ideation. The findings show that profiles of patients who are at high risk of suicide attempts can be effectively identified using ROC, with relatively good sensitivity and specificity.

Adult↗
PubMed2025

CRISPR RNP-Mediated Transgene-Free Genome Editing in Plants: Advances, Challenges and Future Directions for Tree Species.

CRISPR ribonucleoprotein (RNP)-mediated genome editing offers a transgene-free platform for precise genetic modification in diverse herbaceous and tree species, including rice, wheat, apple, poplar, oil palm, rubber tree and grapevine. However, its application in woody plants faces distinct challenges, notably inefficient delivery and regeneration difficulties, particularly in species such as bamboo. While some of these issues also occur in herbaceous plants, they are often significantly more complex in woody species due to factors such as intricate cell wall architecture, widespread recalcitrant genotypes and inherent limitations of current delivery platforms. This review presents the first in-depth, critical re-evaluation of recent advancements in RNP-mediated editing in woody plants, highlighting these obstacles that warrant focused attention. Unlike plasmid-based CRISPR systems, RNP editing utilises Cas9/Cas12a protein-guide RNA complexes without integrating foreign DNA. This enables a DNA-free editing strategy that simplifies regulatory approval and minimises off-target effects due to the transient presence and rapid degradation of RNPs within plant cells. While PEG-mediated protoplast transfection and particle bombardment remain the primary reported methods for RNP delivery in trees, we evaluate promising alternative strategies such as lipofection, electroporation, cell-penetrating peptides and nanoparticle-based systems for targeted RNP delivery. Despite their promise, these advanced methods remain largely untested in woody species. Finally, we outline future research directions, including the development of tree-specific RNP delivery systems and regeneration protocols to enhance efficiency and minimise cytotoxicity. These innovations are essential for unlocking the full potential of RNP-mediated genome editing in long-lived tree species. This review provides a focused and timely roadmap for expanding the application of RNP technology across diverse woody plants.

Gene Editing↗
PubMed1997

Validity of a decision tree for predicting active pulmonary tuberculosis.

The recent outbreaks of multidrug-resistant strains of M. tuberculosis in health care facilities has increased concern over its transmission in health care facilities. Isolation has been recommended for all patients suspected to have tuberculosis even though the feasibility and the cost of this recommendation can be substantial. We have developed a classification tree using clinical and radiographic data from 277 isolation episodes in patients admitted between August 1992 and March 1994 who required isolation for suspicion of tuberculosis. The classification tree was developed with a sensitivity and negative predictive value of 100% by binary recursive partitioning to predict those patients who are unlikely to require isolation. The predictor variables were upper zone disease on chest radiograph, a history of fever, weight loss, and CD4 count. The tree was validated in a separate cohort of 286 isolation episodes between April 1994 and December 1995. In this validation cohort, no erroneous prediction was made of not isolating a patient with active pulmonary tuberculosis. The classification tree had a sensitivity of 100% (95% confidence interval [CI]: 92.5 to 100%), a specificity of 48.1% (95% CI: 43.8 to 52.4%), and a negative predictive value of 100% (95% CI: 98.5 to 100%). We estimate that the use of the tree could have reduced the number of patients requiring isolation by more than 40% without increasing the risk of cross infection.

CD4 Lymphocyte Count↗
PubMed2002

A decision tree for tuberculosis contact investigation.

The University of Alabama at Birmingham and the Alabama Department of Public Health recently developed a logistic regression model showing those variables that are most likely to predict a positive tuberculin skin test in contacts of tuberculosis cases. However, translating such a model into field application requires a stepwise approach. This article describes a decision tree developed to assist public health workers in determining which contacts are most likely to have a positive tuberculin skin test. The Classification and Regression Tree analysis was performed on 292 consecutive cases and their 2,941 contacts seen by the Alabama Department of Public Health from January 1, 1998, to October 15, 1998. Several decision trees were developed and were then tested using prospectively collected data from 366 new tuberculosis cases and their 3,162 contacts from October 15, 1998, to April 30, 2000. Testing showed the trees to have sensitivities of 87-94%, specificities of 22-28%, and false-negative rates between 7 and 10%. The use of the decision trees would decrease the number of contacts investigated by 17-25% while maintaining a false-negative rate that was close to that of the presumed background rate of latent tuberculosis infection in the state of Alabama.

Adult↗
PubMed2000

Production of diagnostic rules from a neurotologic database with decision trees.

A decision tree is an artificial intelligence program that is adaptive and is closely related to a neural network, but can handle missing or nondecisive data in decision-making. Data on patients with Meniere's disease, vestibular schwannoma, traumatic vertigo, sudden deafness, benign paroxysmal positional vertigo, and vestibular neuritis were retrieved from the database of the otoneurologic expert system ONE for the development and testing of the accuracy of decision trees in the diagnostic workup. Decision trees were constructed separately for each disease. The accuracies of the best decision trees were 94%, 95%, 99%, 99%, 100%, and 100% for the respective diseases. The most important questions concerned the presence of vertigo, hearing loss, and tinnitus; duration of vertigo; frequency of vertigo attacks; severity of rotational vertigo; onset and type of hearing loss; and occurrence of head injury in relation to the timing of onset of vertigo. Meniere's disease was the most difficult to classify correctly. The validity and structure of the decision trees are easily comprehended and can be used outside the expert system.

Databases, Factual↗
PubMedDate not supplied

Alternative tree-structured survival analysis based on variance of survival time.

Tree-structured survival analysis (TSSA) is a popular alternative to the Cox proportional hazards regression in medical research of survival data. Several methods for constructing a tree of different survival profiles have been developed, including TSSA based on log-rank statistics, martingale residuals, Lp Wasserstein metrics between Kaplan-Meier survival curves, and a method based on a weighted average of the within-node impurity of the death indicator and the within-node loss function of follow-up times. Lu and others used variance of restricted mean lifetimes as an index of degree of separation (DOS) to measure the efficiency in separations of survival profiles by a classification method. Like tree-based regression analysis that uses variance as a criterion for node partition and pruning, the variance of restricted mean lifetimes between different groups can be an alternative index to log-rank test statistics in construction of survival trees. In this article, the authors explore the use of DOS in TSSA. They propose an algorithm similar to the least square regression tree for survival analysis based on the variance of the restricted mean lifetimes. They apply the proposed method to prospective cohort data from the Study of Osteoporotic Fracture that motivated the research and then compare their classification rule to those rules based on the conventional TSSA mentioned above. A limited simulation study suggests that the proposed algorithm is a competitive alternative to the log-rank or martingale residual-based TSSA approaches.

Aged↗
PubMed2001

Effects of rooting and tree growth of selected woodland species on cap integrity in a mineral capped landfill site.

The above and below ground growth of three tree species (Alnus glutinosa, Pinus nigra var. maritima and Acer pseudoplatanus) was studied on a containment landfill site at Waterford, Hertfordshire, UK. Tree root architecture was studied using soil inspection pits excavated next to 12 trees of each species and mapped in detail. Tree height was related to soil thickness over the compacted mineral cap. No roots entered the cap where soil thickness was 1.3 m, but a few roots, especially of alder, were observed within it when the soil cover was 1.0 m or less. Micromorphological analysis of undisturbed samples of the mineral cap suggested that roots exploited weaknesses in the cap rather than actively causing penetration into it. Alder roots were more tolerant of anaerobic conditions within the cap than the other species examined. The results confirm that mineral caps should be covered by 1.5 m of soil or soil-forming material if tree establishment is intended over a restored landfill site, unless protected by other parts of a composite capping system.

Environmental Pollution↗
PubMed1995

Trees and splines in survival analysis.

During the past few years several nonparametric alternatives to the Cox proportional hazards model have appeared in the literature. These methods extend techniques that are well known from regression analysis to the analysis of censored survival data. In this paper we discuss methods based on (partition) trees and (polynomial) splines, analyse two datasets using both Survival Trees and HARE, and compare the strengths and weaknesses of the two methods. One of the strengths of HARE is that its model fitting procedure has an implicit check for proportionality of the underlying hazards model. It also provides an explicit model for the conditional hazards function, which makes it very convenient to obtain graphical summaries. On the other hand, the tree-based methods automatically partition a dataset into groups of cases that are similar in survival history. Results obtained by survival trees and HARE are often complementary. Trees and splines in survival analysis should provide the data analyst with two useful tools when analysing survival data.

Algorithms↗
PubMed2006

On the typology and the worship status of sacred trees with a special reference to the Middle East.

This article contains the reasons for the establishment of sacred trees in Israel based on a field study. It includes 97 interviews with Muslim and Druze informants. While Muslims (Arabs and Bedouins) consider sacred trees especially as an abode of righteous figures' (Wellis') souls or as having a connection to their graves, the Druze relate sacred trees especially to the events or deeds in the lives of prophets and religious leaders. A literary review shows the existence of 24 known reasons for the establishment of sacred trees worldwide, 11 of which are known in Israel one of these is reported here for the first time. We found different trends in monotheistic and polytheistic religions concerning their current worship of sacred trees.

Anthropology, Cultural↗
PubMed2004

Inhibition of acetylcholinesterase by Tea Tree oil.

Pediculosis is a widespread condition reported in schoolchildren. Treatment most commonly involves the physical removal of nits using fine-toothcombs and the chemical treatment of adult lice and eggs with topical preparations. The active constituents of these preparations frequently exert their effects through inhibition of acetylcholinesterase (AChE, EC 3.1.1.7). Increasing resistance to many preparations has led to the search for more effective treatments. Tea Tree oil, otherwise known as Melaleuca oil, has been added to several preparations as an alternative treatment of head lice infestations. In this study two major constituents of Tea Tree oil, 1,8-cineole and terpinen-4-ol, were shown to inhibit acetylcholinesterase at IC50 values (inhibitor concentrations required to give 50% inhibition) of 0.04 and 10.30 mM, respectively. Four samples of Tea Tree oil tested (Tisserand, Body Treats, Main Camp and Irish Health Culture Association Pure Undiluted) showed anticholinesterase activity at IC50 values of 0.05, 0.10, 0.08 and 0.11 microL mL(-1), respectively. The results supported the hypothesis that the insecticidal activity of Tea Tree oil was attributable, in part, to the anticholinesterase activity of Tea Tree oil.

Acetylcholine↗
PubMed1989

In vivo fixation of atmospheric tritium gas in pine and zelkova trees and their surroundings.

In vivo laboratory experiments on tritium gas (HT) fixation in pine trees were conducted using one-way circuit inhalation apparatus and dwarf pine trees. After 2 hours of exposure to HT, tritium distribution in pine needles, branches, trunk, roots and soil was measured. The specific activity of tritium in pine needles was almost the same as that in the branches and about one fiftieth that in the small roots or soil. To eliminate the contribution of HT oxidation in the soil from the plants, a dwarf pine tree, washed and with its root system sealed, was exposed to HT. Oxidation activity of HT was also determined in in vitro experiments for each part from a dwarf pine tree. Oxidation activity of plant parts above the ground was quite low. In vivo and in vitro experiments were also conducted on dwarf zelkova trees and similar results were obtained.

Atmosphere↗
PubMed2005

Is tea tree oil effective at eradicating MRSA colonization? A review.

In vitro studies show that tea tree oil is capable of killing methicillin-resistant Staphylococcus aureus (MRSA) in a laboratory setting. This review of randomized controlled trials (RCTs) was undertaken to find out whether it is effective at eradicating MRSA colonization compared to standard mupirocin-based regimens in colonized patients. A wide range of databases and internet sources were searched to identify published and unpublished studies. Two RCTs were found that researched the effectiveness of tea tree oil preparations against MRSA. One small RCT (n = 30) showed a large but non-significant improvement at eradicating MRSA compared to traditional treatment, whereas a larger study (n = 224) demonstrated little difference in rates of eradication overall (41% for tea tree and 49% for mupirocin, p = 0.286). However, the larger study found that those with nasal colonization receiving a tea tree regimen were more likely to remain colonized with MRSA in the nose (absolute risk increase 31%, p<0.001). Currently there is insufficient evidence to support the routine use of tea tree oil in clinical practice for eradication of MRSA colonization.

Anti-Infective Agents, Local↗
PubMedDate not supplied

Responses of ABA and CTK to soil drought in leafless and leafy apple tree.

The authors tested the contents of ABA (abscisic acid), ZR (zeatin riboside), DHZR (dihydrozeatin riboside) and iPA (isopentenyl adenosine) in leafless and leafy apple trees (Red Fuji/Malus micromalus Makino) during soil drought stress. ABA concentration in drought stressed leafless trees increased significantly compared to the controls. ABA both in roots and xylem rose steadily in the earlier drought stage, reaching a maximum of 1.46 +/- 0.35 nmol g(-1) FW and 117 nmol l(-1) after the 8th day. Similar change patterns of ABA concentration was observed in the leafy trees during soil drought stress; ABA concentrations in roots and xylem sap increased and reached the maximum in the first three days; after 8th day, it decreased slightly, whereas leaf ABA concentration increased steadily in drought stressed plants throughout the duration of the experiment. Between drought stressed and control trees, no significant differences were observed in concentration of ZR and DHZR in both leafless and leafy trees; whereas iPA concentration of the drought stressed leafless and leafy plants decreased markedly in the later stage of drought. These results showed that endogenous ABA originated mainly from the roots in the earlier drought stage, and mainly from the leaves in the later drought stage. Total CTK showed no reduction in the earlier drought stage and decreased in the later drought stage.

Abscisic Acid↗
PubMed2006

Tree species effects on decomposition and forest floor dynamics in a common garden.

We studied the effects of tree species on leaf litter decomposition and forest floor dynamics in a common garden experiment of 14 tree species (Abies alba, Acer platanoides, Acer pseudoplatanus, Betula pendula, Carpinus betulus, Fagus sylvatica, Larix decidua, Picea abies, Pinus nigra, Pinus sylvestris, Pseudotsuga menziesii, Quercus robur, Quercus rubra, and Tilia cordata) in southwestern Poland. We used three simultaneous litter bag experiments to tease apart species effects on decomposition via leaf litter chemistry vs. effects on the decomposition environment. Decomposition rates of litter in its plot of origin were negatively correlated with litter lignin and positively correlated with mean annual soil temperature (MAT(soil)) across species. Likewise, decomposition of a common litter type across all plots was positively associated with MAT(soil), and decomposition of litter from all plots in a common plot was negatively related to litter lignin but positively related to litter Ca. Taken together, these results indicate that tree species influenced microbial decomposition primarily via differences in litter lignin (and secondarily, via differences in litter Ca), with high-lignin (and low-Ca) species decomposing most slowly, and by affecting MAT(soil), with warmer plots exhibiting more rapid decomposition. In addition to litter bag experiments, we examined forest floor dynamics in each plot by mass balance, since earthworms were a known component of these forest stands and their access to litter in litter bags was limited. Forest floor removal rates estimated from mass balance were positively related to leaf litter Ca (and unrelated to decay rates obtained using litter bags). Litter Ca, in turn, was positively related to the abundance of earthworms, particularly Lumbricus terrestris. Thus, while species influence microbially mediated decomposition primarily through differences in litter lignin, differences among species in litter Ca are most important in determining species effects on forest floor leaf litter dynamics among these 14 tree species, apparently because of the influence of litter Ca on earthworm activity. The overall influence of these tree species on leaf litter decomposition via effects on both microbial and faunal processing will only become clear when we can quantify the decay dynamics of litter that is translocated belowground by earthworms.

Analysis of Variance↗